Are S-Corps Required to Run Payroll?

Running a business means not only focusing on your core products or services but also juggling administrative responsibilities, tax filings, and yes—payroll.

As your business grows, your accountant might recommend changing your business structure to an S-corporation (S-corp) to take advantage of potential tax savings. While that change can be beneficial, it also adds new responsibilities—especially when it comes to payroll.

The good news? Understanding S-corp payroll doesn’t have to be intimidating. In this article, we’ll break down what payroll entails for S-corporations, why it’s essential, and how to navigate the process smoothly.

At Paper Trails, we specialize in guiding small business owners through payroll challenges like these—so you can stay focused on running your business with confidence.

What is an S-Corp?

S-corporations are a unique type of business structure that provides the liability protections of a corporation with some of the tax benefits of a partnership. A key feature of an S-corp is pass-through taxation. This means the company’s profits or losses pass directly through to the owners’ personal tax returns, avoiding the “double taxation” imposed on traditional corporations.

However, this tax-friendly business structure comes with some complexities, particularly when it comes to payroll.

If you’re an owner-employee of an S-corp, the IRS requires you to pay yourself a reasonable salary. This rule is intended to prevent owners from bypassing payroll taxes by paying themselves solely through profit distributions, which aren’t subject to Social Security and Medicare taxes (known as FICA taxes). By paying yourself through payroll, you ensure compliance with tax regulations while demonstrating good business practices.

Why S-Corps Need to Run Payroll

If you’re actively working for your S-corp—whether you’re managing operations, delivering services, or making strategic decisions—you’re considered an employee. As such, the IRS requires you to compensate yourself with a fair, market-based salary. This is where S-corp payroll becomes crucial to compliance.

Skipping payroll or underpaying yourself may save money in the short term, but it puts your business at risk for tax penalties, audits, or worse. The IRS might even reclassify your profit distributions as wages and demand back payments on unpaid payroll taxes. This is a headache you want to avoid.

By running payroll properly, you:

• Stay compliant with IRS regulations.

• Simplify your tax obligations.

• Avoid legal and financial repercussions.

• Maintain credibility with lenders and potential investors.

How to Set Up Payroll for an S-Corp

Running payroll for your S-corp might seem difficult, but it’s quite manageable if you break it into steps. Here’s how you can navigate the process:

1. Obtain an Employer Identification Number (EIN)

Think of your EIN as your business’s Social Security number—it’s how the IRS identifies your company for tax and payroll purposes. You’ll need this number to run payroll, file returns, and open tax accounts.

You can apply for one online through the IRS website. Once you receive it, make sure to keep proof of your EIN on file—either the original IRS EIN letter or a copy of your tax return showing the number. This documentation is essential when setting up accounts and verifying your business with payroll providers like Paper Trails.

2. Open a Business Checking Account

Before running payroll, it’s important to separate your business and personal finances. Open a dedicated business checking account that’s used solely for business transactions.

Payroll funds will always be drawn from this account—not your personal account—and your paycheck will be directly deposited into your personal checking account. This separation simplifies accounting, improves compliance, and keeps your records clean for tax purposes.

3. Set Up Federal and State Payroll Accounts

Even if you’re the sole owner-employee of your S-corp, you’ll need to set up payroll tax accounts at both the federal and state levels. These accounts allow you to:

• Withhold income taxes from your salary.

• Pay Social Security and Medicare taxes (FICA taxes).

• File unemployment taxes (FUTA and SUTA).

• Pay other state tax requirements, such as unemployment tax and Paid Family & Medical Leave (PFML) taxes.

At Paper Trails, we can help you set up all required accounts and make sure your payroll filings are accurate and timely. We’ll also integrate your general ledger with QuickBooks (or other accounting software) and provide your accountant access so they can review filings and reports as needed.

4. Determine a Reasonable Salary

The key to compliance for S-corp owners is paying themselves a reasonable salary. But what does “reasonable” actually mean? According to the IRS, your salary should reflect what you would pay someone else to do the same job. Consider factors like:

• Industry standards for your role.

• Your experience, education, and skills.

• Your time commitment to the business.

• The company’s profitability and financial health.

For example, if you’re running a marketing agency and similar strategists in your area earn $70,000 annually, that figure might serve as a baseline for your salary. The key is to find a balance—underpaying yourself could trigger IRS questions, while overpaying might hurt your business’s finances.

5. Run Payroll Regularly

Once your accounts are ready, it’s time to start paying yourself consistently. Establish a pay schedule (weekly, bi-weekly, or monthly) and stick to it.

At Paper Trails, we recommend running payroll at least monthly to maintain consistent cash flow and simplify bookkeeping. Do not wait until year-end to process payroll—it can create unnecessary stress, tax issues, and cash flow problems.

Each payroll run should include:

• Withholding the correct federal and state taxes.

• Deducting benefits and retirement contributions.

• Keeping payroll records for at least three years.

6. Review Other Key Considerations

In addition to payroll setup, there are a few other compliance items to keep in mind:

• Workers’ Compensation Insurance: Even if you’re the only employee, you may be required to carry workers’ comp coverage. Talk with your insurance agent about whether you can or should exempt yourself.

• Accounting Integration: As mentioned above, we can connect your payroll system to QuickBooks and other accounting platforms for seamless reporting and easier collaboration with your accountant.

• Recordkeeping: Maintain accurate payroll and tax records for at least three years in case of an audit or financial review.

Tax Advantages of S-Corp Payroll

The perks of being an S-corp owner are in the tax advantages that come along with this type of business structure. Unlike sole proprietors or LLC owners who pay self-employment taxes on all income, S-corp owners only pay FICA taxes on their salary—not their distributions. For profitable businesses, this can mean significant tax savings over time.

For example, if your S-corp generates $150,000 in annual profit and you pay yourself a salary of $80,000, you’ll pay FICA taxes on the $80,000 salary. The remaining $70,000 can be distributed as an owner’s draw from the company profits, which isn’t subject to FICA taxes. This approach allows you to reduce your tax burden while staying compliant.

Filing Taxes

Payroll compliance doesn’t stop once you’ve paid yourself. S-corporations must file several key tax forms throughout the year, including:

Form 941: Quarterly payroll tax returns reporting income and FICA taxes withheld.

Form 940: Annual report for federal unemployment taxes (FUTA).

W-2 and W-3 Forms: Year-end summaries of employee wages and taxes withheld, submitted to both employees and the Social Security Administration.

Form 1120S and Schedule K-1: Reports business income, gains, and shareholder distributions.

Keeping accurate records of payroll transactions is essential—not just for tax filing but also in the event of an audit.

S-Corp Payroll FAQs

Do I have to run payroll if I’m the only employee of my S-corp?

Yes. If you actively work in the business—whether that’s managing operations, providing services, or handling clients—you’re considered an employee. The IRS requires you to pay yourself a reasonable wage for the work you perform, even if you’re the only person on payroll.

What happens if I don't pay myself a salary?

Skipping payroll or taking only owner draws may save money short-term, but it can trigger red flags with the IRS. The agency could reclassify your distributions as wages and assess back taxes, penalties, and interest. Paying yourself properly through payroll keeps you compliant and protects your business from unwanted surprises.

How often should I run payroll for my S-corp?

We recommend running payroll at least monthly to maintain consistent cash flow and accurate bookkeeping. Waiting until year-end to “catch up” on payroll can create major tax headaches and make it difficult to manage your business finances throughout the year.

How do I decide what a "reasonable salary" is?

A reasonable salary reflects what you’d pay someone else to perform the same job. Consider your role, experience, time commitment, and the company’s financial health. Industry salary data and conversations with your accountant can also help determine an appropriate figure that satisfies IRS guidelines.

Can I still take "owner's draws" in addition to my salary?

Yes. After paying yourself a reasonable wage through payroll, you can take additional profits as owner distributions. The advantage is that distributions aren’t subject to Social Security and Medicare (FICA) taxes, helping reduce your overall tax burden.

Conclusion

Yes, S-corps run payroll—and it’s an essential part of staying compliant and taking those tax benefits of this unique business structure. By understanding the process, determining a reasonable salary, and filing the necessary taxes, you’ll not only keep the IRS happy but also set your business up for long-term success.

Updated November 2025