Paying federal taxes on an LLC starts with one question: how does the IRS classify your business? A single-member LLC pays through the owner’s personal Form 1040, a multi-member LLC files a partnership return that passes income to each member’s personal return, and any LLC can elect to be taxed as a C-corporation or S-corporation instead. Whichever classification applies, most owners also owe self-employment tax and make quarterly estimated payments during the year rather than a single lump sum at filing. This guide walks through how to pay taxes on an LLC at the federal level: the forms, the payment methods, the deadlines, and the penalties for missing them.
How Your LLC Is Taxed
The IRS has no separate tax category for LLCs. It assigns a default classification based on how many members you have, and you can override that default by filing an election.
A single-member LLC is treated as a “disregarded entity.” The business files no separate return; income and expenses flow onto the owner’s Form 1040.1eCFR. 26 CFR 301.7701-3 – Classification of Certain Business Entities A multi-member LLC defaults to partnership treatment. The LLC files an informational return, but each member reports and pays tax on their share of profits and losses on their own return.2Internal Revenue Service. 2025 Instructions for Form 1065
To be taxed as a C-corporation instead, file Form 8832. The election cannot take effect more than 75 days before the filing date or more than 12 months after it.3Internal Revenue Service. Form 8832 Entity Classification Election A C-corporation pays a flat 21% corporate tax, and distributions to owners are taxed again as dividends on personal returns. To be taxed as an S-corporation, file Form 2553 no later than two months and 15 days after the tax year begins, or at any point during the prior tax year.4Internal Revenue Service. Instructions for Form 2553 S-corporation status keeps pass-through treatment but can lower self-employment taxes, because only the wages you pay yourself are subject to payroll taxes rather than the full profit. The LLC must have no more than 100 shareholders, one class of stock, and only eligible shareholders such as individuals, certain trusts, and estates.5Internal Revenue Service. S Corporations
Federal income tax rates for pass-through owners run from 10% to 37% in 2026.6Internal Revenue Service. IRS Releases Tax Inflation Adjustments for Tax Year 2026
Self-Employment Tax
If your LLC is taxed as a disregarded entity or partnership, you owe self-employment tax on your share of business profits. This is separate from income tax and funds Social Security and Medicare. The combined rate is 15.3%: 12.4% for Social Security and 2.9% for Medicare.7Internal Revenue Service. Self-Employment Tax
The Social Security portion applies only to the first $184,500 of net self-employment income in 2026.8Social Security Administration. 2026 Cost-of-Living Adjustment Fact Sheet Medicare’s 2.9% has no cap, and an additional 0.9% Medicare surtax applies once self-employment income exceeds $200,000, or $250,000 if you’re married filing jointly.9Internal Revenue Service. Topic No. 560, Additional Medicare Tax
You calculate the tax on Schedule SE and attach it to Form 1040. You can then deduct half of the self-employment tax when figuring your adjusted gross income, which reduces the income subject to regular income tax.10Internal Revenue Service. Topic No. 554, Self-Employment Tax
Quarterly Estimated Payments
LLC income isn’t subject to employer withholding, so most owners pay tax in quarterly installments throughout the year. You generally must make estimated payments if you expect to owe $1,000 or more after subtracting withholdings and credits.11Internal Revenue Service. Estimated Taxes The payments cover both income tax and self-employment tax.
The 2026 due dates:
- First quarter: April 15, 2026
- Second quarter: June 15, 2026
- Third quarter: September 15, 2026
- Fourth quarter: January 15, 2027
You can skip the January 15 payment if you file your full 2026 return and pay the balance by February 1, 2027.12Internal Revenue Service. 2026 Form 1040-ES, Estimated Tax for Individuals
To avoid an underpayment penalty, your total estimated payments and withholdings must add up to at least 90% of your 2026 tax liability or 100% of the tax shown on your 2025 return, whichever is smaller. If your 2025 adjusted gross income exceeded $150,000 ($75,000 if married filing separately), the prior-year safe harbor is 110% instead.12Internal Revenue Service. 2026 Form 1040-ES, Estimated Tax for Individuals
The Forms You File
The return you file depends on your classification.
Single-Member LLC
Report business income and expenses on Schedule C, attached to your personal Form 1040.13Internal Revenue Service. 2025 Instructions for Schedule C Schedule C totals your revenue, subtracts cost of goods sold and operating expenses, and produces a net profit or loss that flows to Form 1040 through Schedule 1. If you show a profit, complete Schedule SE for self-employment tax.
Multi-Member LLC
The LLC files Form 1065, reporting the business’s overall income, deductions, and credits. The partnership pays no tax itself.14Internal Revenue Service. About Form 1065 Form 1065 generates a Schedule K-1 for each member showing that person’s share of profits, losses, and credits. Each member reports their K-1 amounts on their individual return and pays the tax there.
LLC Taxed as a Corporation
A C-corporation election means the LLC files Form 1120 and pays 21% on profits. An S-corporation election means filing Form 1120-S, which passes income through to shareholders via Schedule K-1.15Internal Revenue Service. 2025 Instructions for Form 1120 Both corporate forms require detailed balance sheets and reconciliations of book income against taxable income.
How to Send the Payment
Two systems handle nearly all federal tax payments. The Electronic Federal Tax Payment System (EFTPS) is a free Treasury service that accepts every kind of federal tax payment and is the primary system for business entities such as partnerships and corporations.16Bureau of the Fiscal Service. Electronic Federal Tax Payment System Individual taxpayers, including single-member LLC owners filing on Schedule C, can use IRS Direct Pay to pay directly from a bank account with no enrollment. Both systems handle estimated payments, balance-due payments, and extension payments.
You can also mail a check with a payment voucher, but electronic payments give you immediate confirmation and are the safer option for meeting a deadline.
Deadlines and Extensions
Filing deadlines depend on classification. Partnerships (Form 1065) and S-corporations (Form 1120-S) file by the 15th day of the third month after the tax year ends, which is March 15 for calendar-year filers. Individual owners of disregarded entities file Form 1040 by April 15. C-corporations (Form 1120) also file by the 15th day of the fourth month.17Internal Revenue Service. Publication 509 (2026), Tax Calendars
For more time, you can request an automatic six-month extension. Individuals use Form 4868, pushing the deadline to October 15.18Internal Revenue Service. Form 4868 Partnerships and S-corporations use Form 7004, which moves their deadline to September 15.19Internal Revenue Service. Instructions for Form 7004 An extension buys time to file, not time to pay. Interest and possible penalties still run on any tax not paid by the original deadline.
Penalties for Late Filing or Payment
Late filing and late payment carry separate penalties that can stack.
For individual and C-corporation returns, the failure-to-file penalty is 5% of the unpaid tax per month or partial month, capped at 25%. The failure-to-pay penalty adds 0.5% per month. When both apply in the same month, the failure-to-file penalty is reduced by the failure-to-pay amount, so the combined charge stays at 5% per month.20Internal Revenue Service. Failure to File Penalty
Partnership and S-corporation returns work differently: the penalty is per member, not per dollar of unpaid tax. For returns due after December 31, 2025, it’s $255 per month or partial month for each person who was a partner or shareholder during the tax year, for up to 12 months.20Internal Revenue Service. Failure to File Penalty A five-member LLC that files its 1065 four months late would owe $5,100 in penalties (5 × $255 × 4), even if no tax was due at the entity level.
Deductions That Reduce What You Owe
Several deductions can cut the tax you actually pay.
The qualified business income (QBI) deduction under Section 199A lets eligible pass-through owners (sole proprietors, partners, and S-corporation shareholders) deduct up to 20% of qualified business income from a domestic trade or business. It was made permanent by the One Big Beautiful Bill Act.21Internal Revenue Service. Qualified Business Income Deduction C-corporation income doesn’t qualify. Starting in 2026, if you have at least $1,000 in QBI from an active qualified trade or business, you can claim a minimum QBI deduction of $400 even when 20% would come out lower.6Internal Revenue Service. IRS Releases Tax Inflation Adjustments for Tax Year 2026 The full 20% is available without limitation if 2026 taxable income is below $201,750, or $403,500 for married filing jointly; above those thresholds the deduction phases out based on the type of business, W-2 wages paid, and qualified property held.
If you use part of your home regularly and exclusively for business, you can deduct a portion of housing costs. The simplified method is $5 per square foot up to 300 square feet ($1,500 maximum).22Internal Revenue Service. Simplified Option for Home Office Deduction The actual-expense method prorates mortgage interest, utilities, insurance, and repairs by the business percentage of your home.
Self-employed owners who pay their own health coverage can deduct 100% of premiums for medical, dental, and vision insurance for themselves, a spouse, and dependents. The deduction is claimed on Form 7206 and flows to Schedule 1 of Form 1040.23Internal Revenue Service. Instructions for Form 7206 You can’t claim it for any month you were eligible for employer-subsidized coverage through your own job or a spouse’s.
State Taxes Still Apply
Federal is only part of what you owe. Most states impose their own income tax on LLC earnings, and many charge annual fees, franchise taxes, or minimum taxes that apply whether or not the LLC earned income during the year. Amounts vary from nothing to several hundred dollars or more. Check with your state’s department of revenue or secretary of state office. Missing a state obligation can cost your LLC its good standing and, in some states, lead to administrative dissolution.