Tax for physicians

    Tax planning for physicians: W-2, 1099 and locum tenens

    Physicians often mix hospital W-2 pay with moonlighting, locums or expert witness income. Here is how each type of income is taxed, which entity and retirement choices fit, and what multi-state work adds.

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    • Last reviewed October 10, 2026
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    What tax planning should a physician with 1099 income do?

    A physician with 1099 income should set up quarterly estimates, open a self-employed retirement plan, and consider an S corporation only when steady profit supports a reasonable salary. Locums across states adds nonresident returns. Your Virtual CPA, a licensed CPA firm, plans and prepares returns for physicians, CRNAs, NPs and PAs. Request a free consultation to review your income.

    W-2, 1099 and locum tenens income

    • Hospital or group W-2. Taxes are withheld. Your employer pays half of FICA. Unreimbursed job expenses are generally not deductible on your federal return.
    • 1099 moonlighting, locums or expert witness work. Reported on Schedule C. You pay self-employment tax and make estimated payments. Ordinary and necessary business expenses are deductible, such as licenses, malpractice insurance you pay, CME tied to your current work, and business travel away from your tax home.
    • Locums through an agency. Some agencies pay W-2, others 1099. Read the contract. Travel and lodging paid by the agency may be reimbursed under an accountable plan or included in income.
    • Partner or K-1 income. Practice partners report their share from the partnership return and generally pay self-employment tax on it.

    Tax home. Under IRS Publication 463, travel is deductible only when you are away from your tax home. Physicians who work only locums and have no regular base need to check this carefully.

    S corporations and reasonable compensation

    An S corporation can make sense for a physician with substantial, steady 1099 or practice income. Profit above a reasonable salary is not subject to self-employment tax. But the salary must be reasonable for the services you perform. For physicians, reasonable pay is often high, so the savings may be smaller than expected.

    An S corporation also means payroll, a separate Form 1120-S and state filings. See S corp reasonable compensation and S corp accountable plans.

    QBI. Health is a specified service trade or business under Treas. Reg. §1.199A-5(b)(2)(ii). The qualified business income deduction phases out above income thresholds for physician income.

    Retirement plans for self-employed physicians

    IRS Publication 560 covers the three main options.

    • SEP IRA. Employer contributions only, based on net self-employment earnings. Can be set up and funded up to your return due date, including extensions. Simple, but no employee deferral.
    • Solo 401(k). Employee deferrals plus employer contributions. The employee deferral limit is shared with any hospital 401(k) or 403(b) deferrals, because it is one limit per person. A sole proprietor with no employees can adopt one after year end, by the return due date without extensions, but deferral elections for the year must be made by year end.
    • Defined benefit or cash balance plan. Contributions are actuarially determined to fund a target benefit and can be much larger than defined contribution limits for older, high-earning physicians. Requires an actuary and ongoing funding.

    Plans can be combined, with coordination rules. Employees of your practice may need to be covered.

    Multi-state licenses and quarterly estimates

    Holding licenses in several states does not create tax by itself. Working there does. Locums income is generally taxed by the state where you perform the work, and your home state may give a credit. DC, Maryland and Virginia residents who work across the line have their own rules. See live in Virginia or Maryland, work in DC.

    Federal estimates are due in four installments. Higher earners use a 110% of prior-year tax safe harbor when prior AGI exceeded $150,000 ($75,000 MFS), per IRS Publication 505. See quarterly tax planning.

    How it works with us

    Best for: hospital-employed physicians with side income, locum tenens physicians, CRNAs, NPs and PAs, and practice owners.

    1. Free initial consultation. Share your W-2s, 1099s, contracts and states worked.
    2. Fees quoted upfront, in writing. Transparent, fair fees in an engagement letter.
    3. Plan. We map entity, retirement plan and estimate choices to your income.
    4. Setup. If an S corporation fits, we handle the election, payroll and accountable plan.
    5. Returns. We prepare federal, resident and nonresident state returns.

    Own a practice? See medical practice accounting.

    Physician situations, tax issues and planning moves

    Physician situationKey tax issuesPlanning moves
    Hospital W-2 onlyWithholding, 401(k)/403(b) choices, NIIT on investmentsMax workplace plans, backdoor Roth, HSA if eligible
    W-2 plus 1099 moonlightingSelf-employment tax, estimates, shared deferral limitSolo 401(k) or SEP, raise W-2 withholding, Schedule C expenses
    Full-time locum tenens (1099)Tax home, multi-state returns, travelTrack days by state, confirm tax home, quarterly estimates
    Steady, substantial 1099 profitSelf-employment tax on all profitModel an S corporation with reasonable salary and accountable plan
    Practice owner or partnerPayroll, entity returns, QBI limits, state PTETRetirement plan design for staff, PTET election, bookkeeping

    Expert CPAs. Personal attention.

    Physician with W-2, 1099 or locums income? Request a free initial consultation and we'll map out entity, retirement and estimate choices.

    Frequently asked questions

    Neither is automatically better. As a W-2 employee, your employer pays half of Social Security and Medicare and offers benefits. As a 1099 contractor, you pay self-employment tax yourself but can deduct business expenses and set up your own retirement plan. Compare the full package, not just the rate.

    Sometimes. An S corporation can reduce self-employment tax on profit above a reasonable salary, but it adds payroll, a separate return and state filings. The salary must be reasonable for the services you perform, and for physicians that is often high. It tends to make sense only when 1099 profit is substantial and steady.

    Often yes, for your 1099 income. But the employee deferral limit is per person across all plans, so deferrals at the hospital reduce what you can defer in the solo 401(k). Employer contributions from your own business are counted separately, subject to their own limits. IRS Publication 560 explains the rules.

    Travel is deductible only when you are away from your tax home, which is generally your main place of business. If you have no regular place of business or home you keep up, you may have no tax home and no travel deduction. If the agency pays travel, how it is paid matters. IRS Publication 463 covers the rules.

    Usually you file a nonresident return in states where you earn income, and your home state may give a credit for tax paid to those states. Each state has its own filing threshold. Keep a record of days and income by state.

    Health is a specified service trade or business under Treas. Reg. §1.199A-5(b)(2)(ii). The deduction for physician business income phases out above income thresholds, so many high-earning physicians get a reduced deduction or none. Check the current Form 8995-A instructions for the year’s thresholds.

    Federal estimated payments are made in four installments. If you also have W-2 wages, you can raise withholding at your main job instead, since withholding is treated as paid evenly through the year. States have their own estimate rules.