Accounting Policies [Abstract] Accounting Policies [Abstract] Accounts Payable and Accrued Liabilities Disclosure [Text Block] Accrued Expenses Accounts Payable, Current Accounts payable Accrued Liabilities, Current Accrued expenses Total accrued expense Accrued Professional Fees, Current Accrued professional fees Carrying value as of the balance sheet date of obligations incurred through that date and payable for expenses related to research and development. Used to reflect the current portion of the liabilities (due within one year or within the normal operating cycle if longer). Accrued Research And Development Expense Current Accrued research and development expenses Accumulated Other Comprehensive Income (Loss), Net of Tax Accumulated other comprehensive loss Additional Office Space [Member] Additional Office Space [Member] Additional Boston Office Space [Member] Additional Office Space two [Member] Additional Office Space Two [Member] San Diego Office Space [Member] Additional Paid in Capital, Common Stock Additional paid-in capital Adjustments, Noncash Items, to Reconcile Net Income (Loss) to Cash Provided by (Used in) Operating Activities [Abstract] Adjustments to reconcile net loss to net cash used in operating activities: Allocated Share-based Compensation Expense Total stock-based compensation expense Amendment Flag Amendment Flag Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount Total potentially dilutive shares Antidilutive Securities [Axis] Antidilutive Securities [Axis] Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items] Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items] Antidilutive Securities, Name [Domain] Antidilutive Securities, Name [Domain] Assets Total assets Assets [Abstract] Assets Assets, Current Total current assets Assets, Current [Abstract] Current assets: Assets, Fair Value Disclosure Total cash equivalents and marketable securities AUSTRALIA Australia [Member] Debt Securities, Available-for-sale, Accumulated Gross Unrealized Gain, before Tax Gross Unrealized Gains Debt Securities, Available-for-sale, Accumulated Gross Unrealized Loss, before Tax Gross Unrealized Losses Debt Securities, Available-for-sale, Amortized Cost Amortized Cost Debt Securities, Available-for-sale, Current Fair Value Marketable securities Available-for-sale Securities [Table Text Block] Summary of Marketable Securities Business Description and Basis of Presentation [Text Block] Nature of the Business and Basis of Presentation Capital Expenditures Incurred but Not yet Paid Property and equipment included in accounts payable Cash and Cash Equivalents, at Carrying Value Cash and cash equivalents at end of period Cash and cash equivalents at beginning of period Cash and cash equivalents Cash and Cash Equivalents, Fair Value Disclosure Cash equivalents Cash and Cash Equivalents, Period Increase (Decrease) Net decrease in cash and cash equivalents Cash, Cash Equivalents, and Short-term Investments Total cash, cash equivalents and marketable securities Cash Flow, Noncash Investing and Financing Activities Disclosure [Abstract] Supplemental disclosure of non-cash investing and financing activities: Certificates of deposit due within one year. Certificates Of Deposit Due Within One Year [Member] Certificates of Deposit (Due Within 1 Year) [Member] Certificates of Deposit [Member] Certificates of Deposit [Member] Commercial Paper [Member] Commercial Paper [Member] Commercial Paper, Not Included with Cash and Cash Equivalents Due Within One Year [Member] Commercial Paper, Not Included with Cash and Cash Equivalents Due Within One Year [Member] Commercial Paper (Due within 1 Year) [Member] Commitments and Contingencies Commitments and contingencies (Note 7) Commitments and Contingencies Disclosure [Abstract] Commitments and Contingencies Disclosure [Abstract] Commitments and Contingencies Disclosure [Text Block] Commitments and Contingencies Common Stock, Par or Stated Value Per Share Common stock, par value per share Common Stock, Shares Authorized Common stock, shares authorized Common Stock, Shares, Issued Common stock, shares issued Common Stock, Shares, Outstanding Common stock, shares outstanding Common Stock, Value, Issued Common stock, $0.001 par value per share; 115,000,000 shares authorized as of June 30, 2018 and December 31, 2017; 27,578,989 and 27,489,457 shares issued and outstanding as of June 30, 2018 and December 31, 2017, respectively Retirement Benefits [Abstract] Retirement Benefits [Abstract] Compensation Related Costs [Abstract] Compensation Related Costs [Abstract] Comprehensive Income (Loss), Net of Tax, Attributable to Parent Total comprehensive loss Comprehensive Income (Loss), Net of Tax, Attributable to Parent [Abstract] Comprehensive loss: Consolidated Entities [Axis] Consolidated Entities [Axis] Consolidated Entities [Domain] Consolidated Entities [Domain] Corporate Bond Securities [Member] Corporate Bonds [Member] Corporate Debt Securities Due Within One Year [Member] Corporate Debt Securities Due Within One Year [Member] Corporate Bonds (Due within 1 Year) [Member] Counterparty Name [Axis] Counterparty Name [Axis] Credit Facility [Axis] Credit Facility [Axis] Credit Facility [Domain] Credit Facility [Domain] Current Fiscal Year End Date Current Fiscal Year End Date Debt Disclosure [Abstract] Debt Disclosure [Abstract] Debt Disclosure [Text Block] Notes Payable Debt Instrument, Basis Spread on Variable Rate Debt facility interest rate Debt Instrument, Covenant Description Debt facility covenant description Debt Instrument, Description Debt facility description Debt Instrument, Description of Variable Rate Basis Debt facility interest rate description Debt Instrument, Face Amount Aggregate principal balance Maximum borrowings under term loan The fee, as a percentage of the term loan, due as a final payment. Debt Instrument Fee Percentage Debt facility fee percentage Debt Instrument, Increase, Accrued Interest Charges to interest expense of debt outstanding Debt Instrument, Interest Rate During Period Debt facility effective interest rate Debt Instrument, Interest Rate, Effective Percentage Debt facility effective interest rate Debt Instrument [Line Items] Debt Instrument [Line Items] Debt Instrument, Maturity Date Debt maturity date Debt Instrument, Periodic Payment, Interest Interest expense on term loan The aggregate amount of cash permitted to be maintained by the Australian subsidiary. Debt Instrument, Restrictive Covenants, Investment In Subsidiaries Aggregate value of cash maintained by Australian subsidiary, limit Debt Instruments [Abstract] Debt Instruments [Abstract] Schedule of Long-term Debt Instruments [Table] Schedule of Long-term Debt Instruments [Table] Defined Contribution Plan, Cost Contribution expense Defined Contribution Plan Disclosure [Line Items] Defined Contribution Plan Disclosure [Line Items] Defined Contribution Plan, Employer Matching Contribution, Percent of Employees' Gross Pay Percentage of employer's contribution on employee's base salary Defined Contribution Plan [Table] Defined Contribution Plan [Table] Depreciation Depreciation expense Development Based Milestones [Member] Development Based Milestones [Member] Development Based Milestones [Member] Disclosure of Compensation Related Costs, Share-based Payments [Abstract] Disclosure of Compensation Related Costs, Share-based Payments [Abstract] Disclosure of Compensation Related Costs, Share-based Payments [Text Block] Stock-Based Awards Document And Entity Information [Abstract] Document And Entity Information [Abstract] Document And Entity Information [Abstract] Document Fiscal Period Focus Document Fiscal Period Focus Document Fiscal Year Focus Document Fiscal Year Focus Document Period End Date Document Period End Date Document Type Document Type Earnings Per Share [Abstract] Earnings Per Share [Abstract] Earnings Per Share, Basic and Diluted Net loss per share, basic and diluted Earnings Per Share, Policy [Policy Text Block] Net Income (Loss) Per Share The percentage to be refunded pertaining to the tax incentive for qualified research and development activities. Effective Tax Incentive Rate Related To Research And Development Percentage of refundable tax incentive Employee-related Liabilities, Current Accrued payroll and related expenses Employee Stock Option [Member] Options to Purchase Common Stock [Member] Entity Central Index Key Entity Central Index Key Entity Common Stock, Shares Outstanding Entity Common Stock, Shares Outstanding Entity Filer Category Entity Filer Category Entity Incorporation, Date of Incorporation Entity incorporation date Entity Registrant Name Entity Registrant Name Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items] Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items] Fair Value Measurements, Recurring and Nonrecurring [Table] Fair Value Measurements, Recurring and Nonrecurring [Table] Fair Value, Assets Measured on Recurring and Nonrecurring Basis [Table Text Block] Summary of Cash Equivalents and Marketable Securities Fair Value Hierarchy and NAV [Axis] Fair Value Hierarchy and NAV [Axis] Fair Value Disclosures [Abstract] Fair Value Disclosures [Abstract] Fair Value Disclosures [Text Block] Fair Value Measurements and Marketable Securities Fair Value, Inputs, Level 1 [Member] Quoted Prices in Active Markets, (Level 1) [Member] Fair Value, Inputs, Level 2 [Member] Significant Other Observable Inputs (Level 2) [Member] Fair Value Hierarchy and NAV [Domain] Fair Value Hierarchy and NAV [Domain] Foreign Currency Transaction Gain (Loss), before Tax Foreign currency transaction (losses) gains, net Foreign Currency Transaction Gain (Loss), Unrealized Unrealized foreign currency transaction gains (losses) Unrealized foreign currency transaction losses (gains) General and Administrative Expense General and administrative General and Administrative Expense [Member] General and Administrative [Member] Income Statement [Abstract] Income Statement [Abstract] Income Statement Location [Axis] Income Statement Location [Axis] Income Statement Location [Domain] Income Statement Location [Domain] Increase (Decrease) in Accounts Payable Accounts payable Increase (Decrease) in Accrued Liabilities Accrued expenses Increase (Decrease) in Operating Capital [Abstract] Changes in operating assets and liabilities: Increase (Decrease) in Prepaid Expense and Other Assets Prepaid expenses and other current assets The increase (decrease) during the reporting period in tax incentive receivable, which represents the amount due from tax authorities. Increase Decrease In Tax Incentives Receivable Tax incentive receivable Interest Expense Interest expense Interest Paid, Excluding Capitalized Interest, Operating Activities Cash paid for interest Investment Income, Net Interest income Investment Income, Net, Amortization of Discount and Premium Amortization of (discount) premium on marketable securities Investment Type [Axis] Investment Type [Axis] Investments [Domain] Investments [Domain] IPO [Member] Public Offering [Member] Lease Arrangement, Type [Axis] Lease Arrangement, Type [Axis] Lease Arrangement, Type [Domain] Lease Arrangement, Type [Domain] Lease Expiration Date Lease expiration date Lessee, Operating Lease, Renewal Term Lease extension period Liabilities Total liabilities Liabilities and Equity Total liabilities and stockholders' equity Liabilities and Equity [Abstract] Liabilities and Stockholders' Equity Liabilities, Current Total current liabilities Liabilities, Current [Abstract] Current liabilities: Maximum fee the Company is obligated to pay per licensed product. Licensing Fees Per Product Maximum Licensing fees per product maximum The minimum default amount over which the lender may exercise remedies against the Company. Line Of Credit Facility Debt Default Minimum Amount Credit facility default amount Line of Credit Facility, Periodic Payment, Interest Interest expense on credit facility Long-term Debt Total Long-term Debt, Maturities, Repayments of Principal in Year Four 2021 Long-term Debt, Maturities, Repayments of Principal in Year Three 2020 Long-term Debt, Maturities, Repayments of Principal in Year Two 2019 Long-term Debt, Maturities, Repayments of Principal, Remainder of Fiscal Year 2018 Long-term Debt, Type [Axis] Long-term Debt, Type [Axis] Long-term Debt, Type [Domain] Long-term Debt, Type [Domain] Notes Payable, Noncurrent Notes payable, long-term Category of Item Purchased [Axis] Category of Item Purchased [Axis] Long-term Purchase Commitment, Category of Item Purchased [Domain] Long-term Purchase Commitment, Category of Item Purchased [Domain] Marketable Securities, Policy [Policy Text Block] Marketable securities Maximum [Member] Maximum [Member] Amount of payment due for milestones that have been achieved Milestone Liability Milestone payments due Amount of payment due upon reaching milestone. Milestone Payment Amount Milestone payments Minimum [Member] Minimum [Member] Money Market Funds [Member] Money Market Funds [Member] Net Cash Provided by (Used in) Financing Activities Net cash provided by (used in) financing activities Net Cash Provided by (Used in) Financing Activities [Abstract] Cash flows from financing activities: Net Cash Provided by (Used in) Investing Activities Net cash provided by investing activities Net Cash Provided by (Used in) Investing Activities [Abstract] Cash flows from investing activities: Net Cash Provided by (Used in) Operating Activities Net cash used in operating activities Net Cash Provided by (Used in) Operating Activities [Abstract] Cash flows from operating activities: Net Income (Loss) Attributable to Parent Net loss Net loss Net proceeds from sale of securities. Net Proceeds From Sale Of Securities Net proceeds from sale of securities New Accounting Pronouncements, Policy [Policy Text Block] Recently Issued and Adopted Accounting Pronouncements Nonoperating Income (Expense) Total other (expense) income, net Notes Payable Notes payable Notes Payable, Current Notes payable, current Office Space Lease [Member] Office Space Lease [Member] Boston Office Space [Member] Operating Expenses Total operating expenses Operating Expenses [Abstract] Operating expenses: Operating Income (Loss) Loss from operations Operating Leases, Future Minimum Payments Due Total Operating Leases, Future Minimum Payments, Due in Four Years 2021 Operating Leases, Future Minimum Payments, Due in Three Years 2020 Operating Leases, Future Minimum Payments, Due in Two Years 2019 Operating Leases, Future Minimum Payments, Remainder of Fiscal Year 2018 (July - December) The number of options available to extend an operating lease. Operating Leases Number Of Options To Extend Lease Number of options to extend lease Operating Leases, Rent Expense, Net Operating lease, rental expense Operating Leases, Rent Expense, Sublease Rentals Sublease rental income Organization, Consolidation and Presentation of Financial Statements [Abstract] Organization, Consolidation and Presentation of Financial Statements [Abstract] Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items] Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items] Organization Consolidation And Presentation Of Financial Statements Disclosure [Line Items] Organization Consolidation And Presentation Of Financial Statements Disclosure [Table] Organization Consolidation And Presentation Of Financial Statements Disclosure [Table] Organization Consolidation And Presentation Of Financial Statements Disclosure [Table] Other Accrued Liabilities, Current Accrued other Other Assets, Noncurrent Other assets Other Commitments [Line Items] Other Commitments [Line Items] Other Commitments [Table] Other Commitments [Table] Other Comprehensive Income (Loss), Available-for-sale Securities Adjustment, Net of Tax, Portion Attributable to Parent Unrealized gain on marketable securities Other Comprehensive Income (Loss), Net of Tax, Portion Attributable to Parent Total other comprehensive income Other Comprehensive Income (Loss), Net of Tax, Portion Attributable to Parent [Abstract] Other comprehensive loss: Other Income and Expenses [Abstract] Other income (expense): Paid-in-Kind Interest Non-cash interest expense Payables and Accruals [Abstract] Payables and Accruals [Abstract] Payments of Stock Issuance Costs Payment of public offering costs Payments to Acquire Debt Securities, Available-for-sale Purchases of marketable securities Payments to Acquire Property, Plant, and Equipment Purchases of property and equipment Pension and Other Postretirement Benefits Disclosure [Text Block] Retirement Plan The percentage of research and development costs to be reduced. Percentage Reduction Research And Development Costs Percentage of reduction in research and development costs Plan Name [Axis] Plan Name [Axis] Plan Name [Domain] Plan Name [Domain] Pre Commercialization Milestones [Member] Pre Commercialization Milestones [Member] Pre Commercialization Milestones [Member] Preferred Stock, Par or Stated Value Per Share Preferred stock, par value per share Preferred Stock, Shares Authorized Preferred stock, shares authorized Preferred Stock, Shares Issued Preferred stock, shares issued Preferred Stock, Shares Outstanding Preferred stock, shares outstanding Preferred Stock, Value, Issued Preferred stock; $0.001 par value per share; 5,000,000 shares authorized as of June 30, 2018 and December 31, 2017; no shares issued and outstanding as of June 30, 2018 and December 31, 2017 The cash outflow associated with the premium paid on marketable securities. Premium On Marketable Securities Premium on marketable securities, net Prepaid Expense and Other Assets, Current Prepaid expenses and other current assets Proceeds from Issuance Initial Public Offering Net proceeds from public offering, after underwriting discount, commission and estimated offering expenses Net proceeds from public offering, after underwriting discount, commission and offering expenses Proceeds from Issuance of Shares under Incentive and Share-based Compensation Plans, Including Stock Options Proceeds from exercise of common stock options and employee stock purchase plan Proceeds from Notes Payable Proceeds from issuance of notes payable Proceeds from Sale and Maturity of Debt Securities, Available-for-sale Proceeds from sales and maturities of marketable securities Product Commercialization Milestones [Member] Product Commercialization Milestones [Member] Product Commercialization Milestones [Member] Property, Plant and Equipment, Net Property and equipment, net Future cash outflow to pay for costs associated with a public offering. Public Offering Costs Included In Accounts Payable And Accrued Expenses Public offering costs included in accounts payable and accrued expenses Range [Axis] Range [Axis] Range [Domain] Range [Domain] Repayments of Notes Payable Repayments of notes payable Counterparty Name [Domain] Counterparty Name [Domain] Research and Development [Abstract] Research and Development [Abstract] Research and Development Expense Research and development Research and Development Expense [Member] Research and Development [Member] Research and Development Expenses [Table] Research and Development Expenses [Table] Research and Development Expenses [Table] Research and Development Tax Incentive [Line Items] Research And Development Tax Incentive [Line Items] Research and Development Tax Incentive [Line Items] Research, Development, and Computer Software Disclosure [Text Block] Australia Research and Development Tax Incentive Restricted Cash and Investments Loan agreement minimum liquidity required Restricted cash and investments as percentage of outstanding principal amount. Restricted Cash And Investments As Percentage Of Outstanding Principal Amount Percentage equivalent of cash, cash equivalents and marketable securities balance Restricted Stock [Member] Unvested Restricted Common Stock [Member] Retained Earnings (Accumulated Deficit) Accumulated deficit Retirement 401K plan. Retirement 401K Plan [Member] Retirement 401K Plan [Member] Retirement Plan Type [Axis] Retirement Plan Type [Axis] Retirement Plan Type [Domain] Retirement Plan Type [Domain] Revenues Revenue Sale of Stock [Domain] Sale of Stock [Domain] Schedule of Accrued Liabilities [Table Text Block] Schedule of Accrued Expenses Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share [Table] Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share [Table] Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share [Table Text Block] Summary of Common Stock Equivalents Outstanding Debt Securities, Available-for-sale [Line Items] Schedule of Available-for-sale Securities [Line Items] Schedule of Available-for-sale Securities [Table] Schedule of Available-for-sale Securities [Table] Schedule of Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Table Text Block] Summary of Stock-Based Compensation Expense Related to Stock Options and Restricted Common Stock Schedule of Future Minimum Rental Payments for Operating Leases [Table Text Block] Schedule of Future Minimum Lease Payments for Operating Leases Schedule of Maturities of Long-term Debt [Table Text Block] Schedule of Estimated Future Principal Payments Schedule of Share-based Compensation Arrangements by Share-based Payment Award [Table] Schedule of Share-based Compensation Arrangements by Share-based Payment Award [Table] Secured Debt [Member] Secured Debt [Member] Geographical [Domain] Geographical [Domain] Share-based Compensation Stock-based compensation expense Share-based Compensation Arrangement by Share-based Payment Award [Line Items] Share-based Compensation Arrangement by Share-based Payment Award [Line Items] Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant Shares available for grant Share-based Compensation Arrangement by Share-based Payment Award, Options, Other Increases (Decreases) in Period Shares added to plan Shares Issued, Price Per Share Share price per share Significant Accounting Policies [Text Block] Summary of Significant Accounting Policies Simple ira plan. SIMPLE IRA plan [Member] SIMPLE IRA plan [Member] Geographical [Axis] Geographical [Axis] Statement [Line Items] Statement [Line Items] Statement of Cash Flows [Abstract] Statement of Cash Flows [Abstract] Statement of Financial Position [Abstract] Statement of Financial Position [Abstract] Statement [Table] Statement [Table] Stockholders' Equity Attributable to Parent Total stockholders' equity Stockholders' Equity Attributable to Parent [Abstract] Stockholders' equity: Stock Issued During Period, Shares, New Issues Issuance of common stock Sublease area of real estate property. Sublease Area Of Real Estate Property Subleased area Sublease Expiration Date Sublease Expiration Date Sublease expiration date Subsequent Event [Member] Subsequent Event [Member] Subsequent Events [Abstract] Subsequent Events [Abstract] Subsequent Events [Text Block] Subsequent Event Subsequent Event Type [Axis] Subsequent Event Type [Axis] Subsequent Event Type [Domain] Subsequent Event Type [Domain] Subsequent Licensed Product [Member] Subsequent Licensed Product [Member] Subsequent Licensed Product [Member] Subsidiaries [Member] Zafgen Australia Pty Limited [Member] Sale of Stock [Axis] Sale of Stock [Axis] Supplemental Cash Flow Information [Abstract] Supplemental disclosure of cash flow information: Tax incentive receivable. Tax Incentive Receivable Tax incentive receivable The amount expected to be received within one year or the normal operating cycle, if longer, as part of a refundable tax incentive program for research and development activities. Tax Incentive Receivable Current Tax incentive receivable Tax incentive receivable, non current. Tax Incentive Receivable Noncurrent Tax incentive receivable The amount of reduction to research and development expense recorded in the income statement. Tax Incentive Research And Development Activities Reduction to research and development expenses Term Loan [Member] Term Loan [Member] Term Loan [Member] Trading Symbol Trading Symbol Two thousand and fourteen credit facility. Two Thousand And Fourteen Credit Facility [Member] 2014 Credit Facility [Member] Two Thousand Fourteen Stock Option [Member] Two Thousand Fourteen Stock Option [Member] 2014 Stock Option and Incentive Plan [Member] Unrelated Third Party Member Unrelated Third Party Member Unrelated Third Party Member Use of Estimates, Policy [Policy Text Block] Use of Estimates US Government Corporations and Agencies Securities [Member] U.S. Government Securities [Member] Us Government Securities Due Within One Year [Member] Us Government Securities Due Within One Year [Member] U.S. Government Securities (Due within 1 Year) [Member] Weighted Average Number of Shares Outstanding, Basic and Diluted Weighted average common shares outstanding, basic and diluted