How to File New York Form CT-3: Tax Bases, Deadline, and Payment

To file New York Form CT-3, a C-corporation completes its federal return first, then transfers figures to the state form, applies New York additions and subtractions on Form CT-225, calculates tax under three separate bases and pays whichever is highest, adds the MTA surcharge on Form CT-3-M if applicable, and submits electronically by the 15th day of the third-and-a-half month after year-end — April 15 for calendar-year filers. Most of the work is arithmetic once you have the right numbers in front of you. The rest of this guide walks through who files, what to gather, how the tax is computed, when prepayments and the return are due, and how to transmit the return and payment.¹

Confirm You’re the Right Filer

Form CT-3 is for C-corporations subject to Article 9-A. Any corporation incorporated in New York files, regardless of where it does business. A corporation incorporated elsewhere files if it employs capital, owns or leases property, or maintains an office in New York, or if its New York receipts reach $1 million or more in the tax year.²

S-corporations do not use this form. Once the Department of Taxation and Finance approves S-corporation status, the entity files Form CT-3-S instead.³ A corporation that is active but earned no income still files CT-3, because the fixed dollar minimum applies as long as the entity legally exists.

What to Gather Before You Start

CT-3 pulls heavily from the federal return, so finish federal Form 1120 (or the applicable variant such as 1120-REIT or 1120-RIC) first.⁴ Then collect:

The corporation’s Employer Identification Number.
The six-digit NAICS code describing the primary business activity. Acceptable codes are listed in New York Publication 910.
New York addition and subtraction adjustments for Form CT-225. Common additions include state and local taxes deducted federally; common subtractions include income from certain New York State and local bonds.
Investment and exempt income detail for Form CT-3.1, which calculates the investment income subtracted from entire net income and the investment capital subtracted from total assets.⁵
Receipts data broken out by location, detailed enough to compute the New York apportionment factor and to identify the correct fixed dollar minimum bracket.

The return itself is organized into parts: Part 1 captures identifying information and schedule check-offs; Parts 3, 4, and 5 compute the three tax bases; Part 6 compares them and arrives at tax due; and Part 7 applies credits. Most filers attach CT-3.1 and CT-225 at a minimum, plus the specific claim form for any credit claimed.⁴

Calculate Tax Under All Three Bases

New York computes three separate tax amounts and the corporation pays the highest. That is why even a corporation that lost money owes something.

Business Income Base

Start with federal taxable income, apply the New York additions and subtractions from CT-225, and multiply by the business apportionment factor — a single receipts fraction comparing New York receipts to total receipts everywhere. The apportioned income is taxed at 6.5% if the business income base is $5 million or less, or 7.25% if it exceeds $5 million.⁶ Qualified emerging technology companies pay 4.875%, and qualified New York manufacturers pay 0%. The higher 7.25% rate applies to the entire base, not just the amount above $5 million, so corporations near that threshold should check the figure carefully.

Capital Base

The capital base tax is 0.1875% of business capital apportioned to New York, capped at $5 million for general business taxpayers.⁶ Business capital is generally total assets minus investment capital. Qualified New York manufacturers and qualified emerging technology companies pay this base at 0%.

Fixed Dollar Minimum

If neither the income base nor the capital base yields a higher number, the corporation pays a flat amount tied to its New York receipts. The scale runs from $25 for receipts of $100,000 or less up to $200,000 for receipts above $1 billion.⁶ The complete bracket table is printed in the Form CT-3 instructions.

MTA Surcharge

Corporations that do business, own or lease property, maintain an office, or derive receipts from activity within the Metropolitan Commuter Transportation District owe an additional surcharge filed on Form CT-3-M.⁷ The MCTD covers New York City plus Dutchess, Nassau, Orange, Putnam, Rockland, Suffolk, and Westchester counties. First apportion franchise tax to the MCTD using a separate receipts-based percentage, then multiply by 30%.⁸ The surcharge is reported on its own form and typically filed alongside CT-3.

Prepayments You Owe Before Filing

By the time the return is due, much of the tax may already be paid in through two prepayment mechanisms.

If the corporation’s franchise tax after credits in the second preceding tax year exceeded $5,000, it must file Form CT-300 and pay a mandatory first installment for the current year by the 15th day of the third month of the tax year — March 16, 2026 for calendar-year filers in 2026.⁹ The MFI is 25% of the second preceding year’s tax if that tax was between $5,000 and $100,000, and 40% if it was over $100,000. Corporations subject to the MTA surcharge that meet these thresholds pay an MFI for the surcharge on the same form at the same percentage.

Separately, Form CT-400 handles the declaration of estimated franchise tax and its installment payments, covering the remainder of expected liability for the year. A corporation that was not required to file in the second preceding year has no MFI obligation but still files CT-400 for estimated payments.

Deadline and Extension

The return is due on or before the 15th day of the third-and-a-half month after the close of the tax year — April 15 for calendar-year filers.¹ Fiscal-year filers count three and a half months from their own year-end.

Form CT-5 grants a six-month extension to file, not to pay. To secure it, submit CT-5 and pay the properly estimated franchise tax and MTA surcharge by the original due date.¹⁰ The estimated payment must either equal or exceed the tax shown on the prior year’s return (if that was a 12-month year) or equal or exceed 90% of the tax as finally determined for the current year. Underpayment can void the extension and bring late-filing penalties even if CT-5 was filed on time.

Submit the Return and Payment

Most corporations are required to e-file. The electronic filing mandate applies when the corporation prepares its own tax documents without a paid preparer, uses approved e-file software or a computer to prepare the return, and has broadband internet access.¹¹ Tax professionals who prepare returns using approved software under the same conditions must e-file on behalf of their clients. The Department publishes a list of approved software developers for corporation tax e-file.¹²

Corporations that qualify for a waiver from the e-file mandate mail paper returns to:

NYS Corporation Tax
PO Box 15181
Albany, NY 12212-5181¹²

Pay a balance due electronically through your Business Online Services account or by electronic funds withdrawal during the e-file submission. Paper filers with a waiver may pay by check made payable to “Commissioner of Taxation and Finance” and mailed with the return.

Part 7 of CT-3 lists dozens of credit claim forms, including the Investment Tax Credit and the Employment Incentive Credit, each with its own form attached to the return. Review the Part 7 list against the corporation’s activities before you finalize the tax figure, since credits can reduce liability (sometimes refundable, sometimes only down to the fixed dollar minimum) and have their own eligibility rules in the instructions for each credit form.

Penalties and Interest for Missing the Deadline

Late filing costs 5% of the unpaid tax for each month or partial month the return is overdue, capped at 25%. Late payment adds 0.5% per month, also capped at 25%, and runs alongside the late-filing penalty.¹² Interest accrues on any underpayment from the original due date until paid. For the first quarter of 2026, the corporate tax underpayment interest rate is 11% annually, and the rate resets each quarter on the Department’s interest rate page.¹³ Penalties and interest can be abated for reasonable cause.

1
New York State Department of Taxation and Finance. Article 9-A—Franchise Tax on General Business Corporations
2
New York State Senate. New York Tax Law Section 209
3
New York State Department of Taxation and Finance. Instructions for Form CT-3-S New York S Corporation Franchise Tax Return
4
New York State Department of Taxation and Finance. Form CT-3 General Business Corporation Franchise Tax Return
5
New York State Department of Taxation and Finance. Instructions for Form CT-3.1
6
New York State Department of Taxation and Finance. Definitions for Article 9-A Corporations
7
New York State Department of Taxation and Finance. Instructions for Form CT-3-M General Business Corporation MTA Surcharge Return
8
New York State Department of Taxation and Finance. CT-3-M General Business Corporation MTA Surcharge Return
9
New York State Department of Taxation and Finance. Instructions for Form CT-300
10
New York State Department of Taxation and Finance. Instructions for Form CT-5 Request for Six-Month Extension to File
11
New York State Department of Taxation and Finance. Electronic Filing Mandate for Business Taxpayers
12
New York State Department of Taxation and Finance. Instructions for Form CT-3 General Business Corporation Franchise Tax Return
13
New York State Department of Taxation and Finance. Interest Rates 1/01/2026–3/31/2026