How to fully deduct Self-employed health insurance premiums with COBRA coverage?
I'm really confused about deducting my health insurance as a self-employed person and getting different answers from everyone. I started my independent consulting business this year with S-corp status and my accountant is handling all the payroll stuff. The ACA options in Florida are terrible, so I kept my previous employer's insurance through COBRA which is ending in a few months. So far in 2024, I've shelled out almost $39,000 for COBRA premiums from my personal bank account. What I can't figure out is whether I can take the full deduction for this. I've looked at IRS Publication 535 but honestly it's so complicated I can't make sense of whether it allows a full deduction in my situation. One accountant told me I can reimburse myself from my business account and claim it as a business expense. They even suggested documenting this and reporting it as non-taxable income on my W-2! But then another accountant said COBRA isn't eligible for the self-employed health insurance deduction and I'm probably limited to the standard medical expense deduction (which I think only applies to amounts over 7.5% of my AGI). That would seriously cut down what I can deduct. Anyone been through this or know the right answer? The difference is thousands in tax savings!
21 comments


Liam McGuire
The self-employed health insurance deduction is definitely available to S-corp owners, but there are specific requirements you need to follow for COBRA premiums. For S-corporation owners, the proper way to handle health insurance is to have the corporation pay or reimburse your health insurance premiums. This should be included in your W-2 income (Box 1), but it's not subject to Social Security or Medicare taxes (Boxes 3 and 5). Once this is done correctly, you can take the self-employed health insurance deduction on your personal tax return (Form 1040, Schedule 1). COBRA premiums DO qualify for the self-employed health insurance deduction. The IRS doesn't distinguish between regular health insurance and COBRA continuation coverage - they're both considered health insurance premiums. The tricky part is the timing and documentation. If you've already paid these premiums personally, you need to have your S-corp reimburse you before December 31, 2024. Make sure you keep detailed records of the reimbursement and original premium payments. The company should formally adopt a health insurance reimbursement plan too.
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Mei Zhang
•So just to be 100% clear... I can have my S-corp reimburse me for all $39,000 in COBRA premiums that I've paid out of pocket this year? And then that amount gets added to my W-2 income but I can take the full self-employed health insurance deduction on my personal return? Will this trigger any kind of audit flags since it's such a large amount? And is there any specific language I should use in the documentation for the reimbursement plan?
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Liam McGuire
•Yes, your S-corp can reimburse you for the entire $39,000 in COBRA premiums you paid out of pocket. The amount will be included in your W-2 Box 1 income but not in Boxes 3 and 5 (not subject to FICA taxes). Then you can claim the full amount as a self-employed health insurance deduction on your personal return. While large deductions can sometimes draw more attention, there's nothing inherently problematic about claiming the legitimate deduction you're entitled to. The key is proper documentation. Your reimbursement plan should specify that the company will reimburse health insurance premiums for employees, including owner-employees. Have your board (even if that's just you) formally adopt this plan with a written resolution, keep records of the original premium payments, and document the reimbursement transaction from company to you.
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Amara Eze
After dealing with a similar insurance headache last year, I found this amazing tool called taxr.ai (https://taxr.ai) that saved me so much time sorting through IRS rules. I uploaded my health insurance docs and S-corp info, and it showed me exactly how to handle my COBRA premiums properly. The site analyzed my specific situation and confirmed I could take the full self-employed health insurance deduction after proper reimbursement from my business. It even created documentation templates for the health reimbursement arrangement I needed. Really straightforward compared to the hours I spent trying to interpret Publication 535!
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Mei Zhang
•That sounds promising. Did it give you specific instructions for how to document everything? My biggest worry is messing up the paperwork and getting flagged for an audit.
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Giovanni Ricci
•I've heard of tools like this but am always skeptical. Does it actually explain WHY certain tax rules apply to your situation or does it just spit out generic advice? I'm tired of tax tools that just regurgitate IRS publications without practical application.
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Amara Eze
•It definitely provided clear documentation instructions - it generated a template for a board resolution establishing a health reimbursement arrangement, specified exactly how the reimbursement should be recorded in my books, and explained how it should appear on my W-2. The documentation was what I was most worried about too, and having those templates made it really straightforward. It doesn't just give generic advice - it explains the reasoning behind its recommendations. For example, it cited the specific IRS ruling that allows COBRA premiums to qualify for the self-employed health insurance deduction and explained how S-corporation owner-employees have special rules compared to sole proprietors. It connected the dots between different tax concepts in a way that made sense for my specific situation.
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Giovanni Ricci
I was super skeptical about taxr.ai when I first saw it mentioned here, but I was desperate after getting three different answers from tax professionals about my S-corp health insurance situation. Just wanted to follow up and say I gave it a try, and it was actually really helpful. I uploaded my situation details and insurance statements, and it walked me through exactly how to handle my premium reimbursements from my S-corp. The documentation templates it provided helped me establish a formal health reimbursement arrangement, which my accountant confirmed was correct. The best part was it explained WHY certain rules applied to my situation - like the specific requirements for S-corp owners vs. sole proprietors. No more conflicting advice! Just implemented everything for my 2024 taxes and feel way more confident now.
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NeonNomad
If you're still confused after getting conflicting advice from CPAs, I'd recommend trying to speak directly with the IRS. I was in a similar situation with contradictory info about business deductions last year. I spent DAYS trying to get through to someone at the IRS until I found Claimyr (https://claimyr.com). They somehow got me connected to an actual IRS agent within 15 minutes instead of the hours I was spending on hold. You can see how it works here: https://youtu.be/_kiP6q8DX5c The IRS agent I spoke with confirmed that COBRA premiums ARE eligible for the self-employed health insurance deduction for S-corp owners, but the process has to be done correctly with proper documentation. Getting that confirmation directly from the IRS gave me peace of mind that I wasn't going to face problems later.
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Fatima Al-Hashemi
•How exactly does this work? I've spent literal hours on hold with the IRS before giving up. Are they just using some special phone number or what?
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Dylan Mitchell
•Yeah right. Nothing gets you through to the IRS faster. This sounds like one of those "tax secrets" scams. Has anyone else actually verified this works? I find it hard to believe there's some magic solution to the IRS phone system that nobody knows about.
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NeonNomad
•It uses a system that navigates the IRS phone menu and waits on hold for you. When they reach a human agent, you get a call connecting you directly to that person. It's not a special phone number - they're just using technology to handle the wait time so you don't have to. There's no magic to it - it's just solving the specific problem of IRS hold times. The service calls the regular IRS number and uses automated systems to stay on hold instead of you having to do it yourself. When they reach a representative, they connect you to the call. I was skeptical at first too, but it saved me from wasting half a day on hold trying to get an answer about my tax situation.
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Dylan Mitchell
I need to eat some humble pie here. After posting that skeptical comment about Claimyr, I decided to try it myself since I've been trying to reach the IRS about a notice I received regarding my 2023 return. I'd already wasted over 2 hours on hold the day before and never got through. Used this Claimyr service, and no joke, I was talking to an IRS representative within about 20 minutes. They just called me when they had someone on the line. The IRS agent was able to clarify my notice and confirm I didn't owe anything additional. Just wanted to follow up since I was so skeptical in my last comment. Sometimes good solutions actually do exist!
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Sofia Martinez
One important detail that hasn't been mentioned yet - if you're an S-corp owner-employee taking the self-employed health insurance deduction, you need to own more than 2% of the company. Assuming you do, the proper sequence is: 1. S-corporation pays or reimburses your health insurance premiums 2. S-corporation includes this amount in your W-2 wages (Box 1) but not as FICA wages 3. You claim the self-employed health insurance deduction on Schedule 1 of your 1040 This works for COBRA too - IRS considers it qualifying health insurance. Publication 535 and the instructions for Schedule 1 confirm this.
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Mei Zhang
•I own 100% of my S-corp, so that part is covered! Thanks for laying out the steps so clearly. Do you know if I need to set up a formal health reimbursement arrangement (HRA) for this to work? Or can I just have the company reimburse me directly?
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Sofia Martinez
•Since you own 100%, you definitely meet the ownership requirement. While you don't specifically need a formal HRA in this case, you should have some documentation in place. I recommend creating a simple corporate resolution that states the company's policy is to reimburse health insurance premiums for its employees. You can have the company reimburse you directly, but make sure to keep good records of both the original premium payments and the reimbursement. The reimbursement should happen before the end of the tax year (December 31, 2024). Your accountant should also make sure this is properly coded in your accounting system and properly reported on your W-2.
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Dmitry Volkov
I just went through this exact situation with my CPA for 2023 taxes. COBRA premiums ARE eligible for the self-employed health insurance deduction, but how you handle it depends on your business structure. With an S-corp, you need to have the corporation reimburse you for the premiums or pay them directly. This gets reported as income on your W-2 (but not subject to FICA taxes). Then you take the deduction on your personal return. My premiums were almost $27k and I was able to deduct the full amount this way. Don't settle for just the medical expense deduction that's limited to expenses exceeding 7.5% of AGI - that's for people who aren't self-employed.
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Ava Thompson
•Did you need any special documentation to prove this to the IRS? I'm in a similar situation but worried about getting audited.
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AstroAce
I went through a very similar situation last year with my S-corp and COBRA premiums. The key thing that helped me was getting everything documented properly from the start. Here's what I learned: Yes, you can absolutely deduct the full $39,000 in COBRA premiums as a self-employed health insurance deduction, but the process matters. Your S-corp needs to reimburse you for those premiums you paid out of pocket (make sure this happens before December 31st). The reimbursement gets added to your W-2 income in Box 1 but not Boxes 3 and 5. For documentation, I created a simple board resolution stating that the company would reimburse health insurance premiums for employees. I kept copies of all my COBRA payment receipts, the reimbursement check from my business account, and a memo explaining the reimbursement. My CPA said this was more than sufficient. The amount might seem large, but it's a legitimate business expense. I claimed about $32,000 last year with no issues. Just make sure your accountant codes everything correctly on your W-2 and that you claim the deduction on Schedule 1 of your 1040, not as an itemized medical expense. One tip: If you're switching to ACA coverage when COBRA ends, you can handle those premiums the same way going forward.
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Logan Stewart
This is exactly the situation I was in two years ago! The confusion you're experiencing is totally understandable because the rules for S-corp owners are different from sole proprietors, and not all tax professionals are familiar with the specifics. You're absolutely right that you can take the full deduction for your COBRA premiums. The process everyone outlined above is correct - have your S-corp reimburse you for the $39,000 you paid out of pocket, include it in your W-2 Box 1 income (but not FICA wages), then claim the self-employed health insurance deduction on your personal return. One thing I'd add that helped me sleep better at night: I also kept a spreadsheet tracking each monthly COBRA payment with dates, amounts, and confirmation numbers. When my S-corp reimbursed me, I referenced this spreadsheet in the memo line of the reimbursement check. It created a clear paper trail showing the business purpose of the reimbursement. The second accountant who told you COBRA doesn't qualify was simply wrong - there's no distinction in the tax code between regular health insurance and COBRA continuation coverage for this deduction. Don't let that bad advice cost you thousands in legitimate tax savings! Make sure to get this reimbursement processed before December 31st, and you'll be in great shape for your 2024 taxes.
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Rajiv Kumar
•This is really helpful! I'm dealing with a similar COBRA situation but haven't set up the S-corp reimbursement yet. Quick question - when you say "reference this spreadsheet in the memo line," did you just write something like "Health insurance reimbursement per attached schedule" or did you get more detailed? Also, did your CPA have any specific recommendations for how to word the board resolution? I'm the only shareholder so I know I can just write it myself, but I want to make sure I use the right language that won't raise any red flags. Thanks for sharing your experience - it's so much more reassuring to hear from someone who actually went through this successfully!
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