Tax Checklist for Doctors: What Physicians Need to File

If you're a doctor preparing to file your taxes, you already know tax season isn’t just about collecting a W-2 and hitting submit. Many physicians have complex financial lives, generating income from employment, consulting, practice ownership, and their investments. On top of that, New York’s state and city tax systems bring their own set of deadlines, elections, and forms.

At Revonary, we work with doctors across New York and beyond to simplify the process, reduce tax liability, and create year-round strategies that support long-term financial goals. This checklist outlines what you need to file your taxes and explains how you can stay ahead of common pitfalls.

Income Documentation: Know Where Your Earnings Came From

Physicians frequently have income from multiple sources. That might include full-time hospital employment, consulting work you do on the side, or distributions you receive from a medical group partnership. The IRS expects documentation for each type, and so does your CPA.

If you are an employee, you’ll have received a W-2. If you earned freelance income from speaking engagements, telemedicine platforms, or locum tenens work, you should receive a 1099-NEC. If you're part of a partnership or S corporation, you’ll also receive a K-1 outlining your share of the business’s income and expenses. Investment income, such as interest, dividends, or capital gains, will be reported on the appropriate 1099 forms.

Missing even one of these forms can result in underreporting income and triggering IRS scrutiny. Taking an organized, methodical approach to keeping track of your tax documents sets the tone for a smooth filing.

Practice Financials and Expense Documentation

If you own or co-own a practice, you'll need more than just your personal tax documents. Your tax advisors require your profit and loss statement, a balance sheet showing assets and liabilities, and general ledger data detailing the business's financial activity. If you don’t have those readily available, it might be worth considering working with an accounting and bookkeeping partner who’ll help you get back on track. 

Supporting documentation is equally important. That includes receipts and logs for CME courses, medical equipment purchases, staff payroll, rent, insurance premiums, and technology subscriptions. If you formed a new entity or made structural changes to your practice, like converting to an S corporation, those formation documents and ownership records will also be required.

Proper recordkeeping ensures you can claim all allowable deductions and defend them in the event of an audit.

Retirement Plans and Health Contributions

Retirement contributions are one of the most valuable tax planning tools available to doctors, especially those in high-income brackets. But to receive the deduction for your contributions, the IRS requires precise reporting.

If you contributed to a Solo 401(k), SEP IRA, or defined benefit plan, be ready to report both the employee and employer portions. HSA and FSA contributions should also be documented in full, especially if you’re using those to reduce your adjusted gross income.

If you’re self-employed and pay for your own health insurance, those premiums may be deductible too, as long as the policy was established in the name of your business. These figures play a key role not only in your tax return, but also in determining eligibility for other deductions such as the Qualified Business Income (QBI) deduction.

Related: QBI Adjustment for Retirement Plan Deduction: What Business Owners Need to Know

State and Local Filing Requirements for New York Doctors

Federal taxes are only part of the equation for New York physicians. You’ll also need to comply with state and city-level filing rules;many of which have different deadlines and documentation requirements.

If you’re part of a pass-through entity that elected into New York’s Pass-Through Entity Tax (PTET) regime, your business was required to make that election by March of the tax year in question, and will need to file the PTET return early the next year. 

Even if you take the standard deduction on your federal return, New York allows you to itemize separately using Form IT-196. This lets you deduct certain expenses, including unreimbursed medical and dental costs, mortgage interest, investment-related fees, and charitable contributions. To take advantage of this opportunity, keep careful records of these costs throughout the year.

More information is available via Form IT-196 instructions.

Estimated Tax Payments and 2025 Deadlines

Physicians who earn income outside of W-2 wages often need to make quarterly estimated payments. If you underpaid throughout the year, the IRS may assess a penalty, even if you pay the full amount by the April deadline.

Here are the relevant dates to keep in mind:

2025 Estimated Tax Deadlines:

• April 15, 2025 (Q1 2025)
• June 17, 2025 (Q2 2025)
• September 16, 2025 (Q3 2025)
• January 15, 2026 (Q4 2025)

If your income was uneven across the year, you may be eligible to use the annualized income installment method on Form 2210 to reduce or eliminate underpayment penalties.

Forms Doctors May Need to File

Depending on how your income is structured, you may be responsible for filing several types of returns:

Business Entities

• Form 1120S – S Corporation return (due in mid-March)
• Form 1065 – Partnership return (due in mid-March)

Individual and State Returns

• Form 1040 – Federal individual income tax return (due in mid-April)
• Form IT-201 – New York State individual return
• Form IT-204-LL – Partnership filing fee (if applicable)
• New York City UBT – For sole proprietors and partnerships operating in NYC

Extensions

Many of our clients choose to file a tax extension. It’s a move that can be beneficial for many reasons, especially if you have a new tax professional or a particularly complex return to file. If you choose to file an extension, here are the dates to be aware of:

• Form 4868 – Extension for individual returns (extends deadline to mid-October)
• Form 7004 – Extension for business returns (extends to mid-September or mid-October depending on entity)

Don’t forget: even if you file for an extension, payment is still due by the original deadline.

Don’t Let Tax Season Derail Your Practice

Taxes for physicians are high-stakes. The financial impact of missed deductions, misclassified income, or late filings can be substantial. Worse, many doctors overpay simply because they don’t have time to stay on top of evolving rules and deadlines. That’s particularly true in a state like New York, where tax law is both aggressive and highly detailed.

At Revonary, we help healthcare professionals build robust, compliant tax strategies that go beyond just checking the boxes. We understand the structure of medical practices, the interplay between personal and business returns, and the state-specific nuances that too many advisors overlook.

If you're ready to learn more about our accounting and tax services for doctors, get in touch with our team today.