How to Pay S-Corp Estimated Taxes: A Quarterly Planner

Staying on top of your S-Corp estimated taxes is one of the most important financial habits you can build as an owner. Unlike a W-2 employee whose entire tax bill is covered by withholding, an S-Corp owner usually has two streams of income — a salary with withholding, and pass-through profit with none — and the IRS expects tax on that profit to be paid in four installments during the year. With the first two 2026 installments already behind us, the next deadline is September 15, 2026, and the final one lands on January 15, 2027. Here is exactly who owes what, when, and how to pay it without triggering a penalty.

Who Actually Pays S-Corp Estimated Taxes

S-Corps are pass-through entities: with narrow exceptions, the corporation itself pays no federal income tax. Profits flow through to each shareholder in proportion to ownership and are taxed on the shareholder’s Form 1040. So the estimated tax obligation belongs to you personally, not the corporation. Per the IRS’s estimated taxes page, individuals — explicitly including S corporation shareholders — generally must make estimated payments if they expect to owe $1,000 or more when they file.

There is one entity-level wrinkle worth knowing. Under the Form 1120-S instructions, the S-Corp itself must make installment payments only if it expects to owe $500 or more of certain corporate-level taxes: the built-in gains tax (Section 1374), the excess net passive income tax (Section 1375), or investment credit recapture. Those generally hit corporations that recently converted from C-Corp status. For most S-Corps that have always been S-Corps, there is nothing to pay at the entity level — everything runs through the shareholders’ personal quarterly payments.

The 2026 Quarterly Payment Schedule

For tax year 2026, the 2026 Form 1040-ES sets four due dates. Payment 1: April 15, 2026, covering income from January through March. Payment 2: June 15, 2026, covering only April and May. Payment 3: September 15, 2026, covering June through August. Payment 4: January 15, 2027, covering September through December. When a due date falls on a weekend or legal holiday it shifts to the next business day, but none of the 2026 dates need shifting — all four fall on weekdays as written.

Notice the quarters are not really quarters: the second period is two months and the fourth is four. If your income is uneven across the year, that mismatch matters for cash-flow planning. One quirk in your favor: the Form 1040-ES instructions let you skip the January 15, 2027 installment entirely if you file your 2026 return and pay the full balance by February 1, 2027.

Safe Harbors: How Much to Pay to Avoid a Penalty

Projecting your exact current-year liability is hard when profit fluctuates, so the law gives you targets keyed to numbers you already know. Under Section 6654, you avoid the underpayment penalty by paying in, through withholding and timely installments, the smaller of: 90% of your 2026 tax, or 100% of the tax shown on your 2025 return — bumped to 110% of the 2025 tax if your 2025 adjusted gross income was over $150,000 ($75,000 if married filing separately for 2026). No penalty applies at all if you end up owing less than $1,000 after withholding, or if you had no tax liability in 2025 as a full-year U.S. citizen or resident.

For most established S-Corp owners, the prior-year safe harbor is the workhorse: take your 2025 total tax, multiply by 100% or 110%, subtract expected 2026 withholding, and divide the rest by four. Meet that number on time each quarter and the penalty math cannot touch you, even if 2026 turns out to be a blowout year and you owe much more in April. The 90% current-year route makes more sense when income has dropped sharply from last year.

What the Underpayment Penalty Actually Costs

The Section 6654 penalty is really interest by another name. It runs on each underpaid installment, from that installment’s due date until it is paid, at the underpayment rate set quarterly under Section 6621 — the federal short-term rate plus three percentage points. That rate is 7% for the third quarter of 2026 (it was 6% in Q2), per the IRS’s quarterly interest rates table, and the IRS announced on August 21, 2026 that it stays at 7% for the fourth quarter (Rev. Rul. 2026-15). Because each installment is tested separately, paying your full balance by April 15, 2027 does not erase a penalty that already accrued on a missed September installment.

One powerful catch-up tool: under Section 6654(g), tax withheld from wages is treated as paid in four equal parts across the year, no matter when it actually came out of your paycheck. Since you are on your own S-Corp’s payroll, cranking up withholding on your remaining 2026 paychecks can retroactively cure an underpayment from the first quarter in a way a late estimated payment never can. This is one of the cleanest levers an S-Corp owner has, and it pairs naturally with a year-end reasonable salary review.

How to Pay S-Corp Estimated Taxes in 2026

Because these are personal payments, use the IRS’s individual channels, listed on the IRS payments page. IRS Online Account lets you pay estimated tax, see your payment history, and confirm prior quarters actually posted — the single most useful feature at filing time. Direct Pay pulls from your bank account free of charge, with no enrollment, and lets you schedule payments up to a year in advance. Debit or credit card works but carries processing fees. Mailing a check with a Form 1040-ES voucher still works too; the postmark date counts.

A note if older articles pointed you to EFTPS for personal payments: per the IRS EFTPS page, individual taxpayers can no longer create new EFTPS accounts. Existing individual enrollees can keep using it for now, but new filers should use Online Account or Direct Pay instead. EFTPS remains the standard rail for your corporation’s business-side deposits.

Don’t Confuse Estimated Taxes With Payroll Taxes

A distinction that trips up many owners: S-Corp estimated taxes are entirely separate from the payroll tax deposits your corporation makes on your W-2 salary. Payroll taxes run through your payroll system on their own deposit schedule under the business’s EIN. Quarterly estimated payments cover your personal income tax on pass-through profit, under your SSN. Both must be current, and a payment made in the wrong system does not credit the other. And if your state has a pass-through entity tax election, entity-level PTET payments follow yet another calendar — see our state-by-state PTET guide.

With September 15 approaching, now is the moment to true up: compare what you have paid so far against your 2026 safe harbor number, factor in how OBBBA’s changes are moving your 2026 liability, and adjust the remaining two installments. Fixing course in September is far cheaper than walking into April with an outsized balance and a 7% penalty clock that has been running since spring. If you would like help running the numbers, contact us.