The fastest way to pay payroll taxes online is through the IRS's Electronic Federal Tax Payment System (EFTPS), which lets you schedule payments directly from your bank account

EFTPS is free and available 24/7. You enroll once, then log in to schedule payments whenever you need to. The IRS also accepts online payments through approved third-party processors — companies like PayUSA, Payroll.com, and others that charge a fee but may integrate with your payroll software. If you use payroll software like QuickBooks, ADP, or Gusto, you can often pay directly through that platform, which routes the payment to the IRS on your behalf.

The method you choose depends on whether you want to manage payments yourself (EFTPS) or let your payroll system handle it automatically. Both reach the IRS the same way and both count as on-time if submitted by the important date.

Key Takeaways

  • EFTPS is the IRS's free payment system and requires a one-time enrollment that takes about 10 minutes online or by phone.
  • You can schedule payments up to 120 days in advance through EFTPS, which is useful if you want to automate your tax calendar.
  • Third-party payment processors charge a fee (usually 0.5% to 2% of the payment) but may be worth it if your payroll software integrates with them.
  • Payroll software like QuickBooks and ADP can pay taxes automatically on your behalf, deducting the payment from your bank account on the due date.
  • The IRS important date for payroll tax deposits is the same whether you pay online or by check — missing it triggers penalties even if you pay the next day.

Setting up EFTPS for the first time

Go to eftps.gov and click "Enroll Now" to create an account. You will need your Employer Identification Number (EIN), Social Security Number if you are a sole proprietor, and your bank account details. The IRS will send you an enrollment confirmation by mail within 5 to 7 business days, which includes a Personal Identification Number (PIN) you use to log in.

If you prefer not to enroll online, you can call the EFTPS helpline at 1-800-555-3453 and enroll by phone. A representative will walk you through the same information and mail your PIN. Either way, you cannot make payments until you receive the PIN in the mail, so plan ahead if you have a payment due soon.

Once you have your PIN, log back into eftps.gov, and you can schedule payments when ready. The system shows you your payment history and lets you see which deposits have been received by the IRS.

How to schedule a payment in EFTPS

Log in with your EIN and PIN. Click "Make a Payment" and select the tax type — for payroll, this is usually "Form 941" (federal income tax withholding and Social Security and Medicare taxes) or "Form 944" if you file annually instead of quarterly. Enter the payment amount and the date you want the money to leave your bank account.

EFTPS requires you to submit the payment at least one business day before the money actually transfers. So if your important date is Friday, you must submit by Thursday. The system will not let you submit a payment for the same day. Once submitted, you receive a confirmation number — save this in case you need to prove the payment was made on time.

You can schedule payments up to 120 days in advance, which means you can set up your entire quarter's deposits at once if you know your payroll amounts. Many business owners do this on the first day of the quarter to avoid missing a important date.

Using payroll software to pay taxes automatically

If you use QuickBooks Payroll, ADP, Gusto, Paychex, or similar software, you can usually authorize the system to pay your taxes on your behalf. During setup, you connect your bank account and tell the software which taxes to pay and when. The software then deducts the payment automatically on each due date and sends it to the IRS.

This approach removes the step of logging into EFTPS yourself, but you are still responsible for making sure the software has the correct amounts and due dates. Review your payroll tax calendar in the software before the quarter starts, and verify that the amounts match what you calculated. If the software makes an error, the IRS will still assess penalties to you, not the software company.

Most payroll software charges a monthly fee that includes tax payments, or charges per payment (usually $5 to $15). This is separate from the fee you pay for payroll processing itself. Check your software's pricing page to see whether payments are included or cost extra.

Paying through third-party payment processors

Companies like PayUSA, Payroll.com, and IRS-approved payment agents let you pay payroll taxes through their websites. You enter your EIN, the payment amount, and your bank account information, and they route the payment to the IRS. These processors charge a fee — typically 0.5% to 2% of the payment amount — which you pay in addition to the tax itself.

The advantage is convenience: some processors integrate with payroll software, so you can pay without leaving your payroll platform. The disadvantage is cost. For a $10,000 quarterly tax payment, a 1% fee adds $100 to your cost. Over a year, that is $400 to $800 in fees you would not pay through EFTPS.

Use a third-party processor only if your payroll software requires it or if you cannot access EFTPS for some reason. Otherwise, EFTPS is the lowest-cost option.

What happens if you miss the important date

If you do not pay by the due date, the IRS assesses a failure-to-pay penalty of 0.5% of the unpaid tax per month, plus interest on the unpaid amount. The penalty starts the day after the important date and compounds monthly. A $10,000 payment due on April 15 that you pay on May 15 costs you about $100 in penalties plus interest.

Paying online does not change the important date. Whether you use EFTPS, payroll software, or a third-party processor, the IRS considers the payment made on the date it is received, not the date you submit it. This is why EFTPS requires you to submit one business day early — to give the system time to process the transfer.

If you realize you will miss a important date, pay as soon as possible anyway. The penalty is smaller if you pay late than if you do not pay at all. You can also request a penalty waiver from the IRS if you have a reasonable cause (such as a serious illness or natural disaster), but you must request it in writing within a certain timeframe.

Reconciling your payments with your tax return

After you pay, the IRS records the payment against your account. When you file your quarterly Form 941 or annual Form 944, the IRS matches the deposits you reported on the form to the payments you made. If the amounts do not match, you may owe additional tax or receive a refund.

Keep your EFTPS confirmation numbers and bank statements showing the payment dates and amounts. If the IRS ever questions a payment, you can prove it was made on time. Many business owners print their EFTPS payment history at the end of the year and attach it to their tax file.

If you overpay during the year — for example, if you pay more in estimated taxes than you actually owe — you can request a refund or carry the overpayment forward to the next quarter. The IRS will not automatically refund overpayments, so you must request it on your tax return or by calling the IRS.

Frequently Asked Questions

Can I pay payroll taxes with a credit card online?

No. The IRS does not accept credit card payments for payroll taxes through EFTPS. You must pay from a bank account (checking or savings). Some third-party processors accept credit cards, but they charge a higher fee to cover the credit card processing cost, making it more expensive than paying by bank transfer.

What if I pay the wrong amount by mistake?

If you overpay, the IRS will hold the extra money and explore it to your next tax period, or you can request a refund. If you underpay, you owe the difference plus penalties and interest. Either way, contact the IRS as soon as you notice the error. You can call the business line at 1-800-829-1040 or log into EFTPS to see your payment history and confirm what was received.

Do I need to enroll in EFTPS if my payroll software pays taxes for me?

No. If your payroll software handles payments automatically, you do not need to set up EFTPS yourself. The software enrolls in EFTPS on your behalf and uses it to send payments. You only need to enroll directly if you want to manage payments yourself.

How far in advance can I schedule a payment in EFTPS?

You can schedule payments up to 120 days in advance. This means on January 1, you can schedule all of your quarterly payments for the entire year if you know your payroll amounts. Many business owners do this to may support they never miss a important date.

What if my bank account information changes?

Log into EFTPS and update your bank account details in the "Manage Account" section. The change takes effect for your next scheduled payment. If you have a payment scheduled for the next few days, call the EFTPS helpline at 1-800-555-3453 to make sure the old account is not charged.