Medical Expense Deduction (医療費控除) in Japan: Claim It After Childbirth

First: Year-End Adjustment vs. Filing Yourself

If you're a regular employee in Japan, your income tax is handled through 年末調整 (nenmatsu chōsei — year-end adjustment). Every December, your employer recalculates the tax you owe for the year, compares it against what was withheld from your monthly pay, and refunds or collects the difference. For most employees, this means you never file a tax return at all — the company does it for you.

Year-end adjustment covers a lot: your basic deduction, dependents, insurance premiums, and so on. But there are a few things it can't handle — and the medical expense deduction is the big one. To claim it, you file a 確定申告 (kakutei shinkoku — a tax return) yourself, separately from what your company does.

Year-end adjustment covers most deductions automatically — but not the medical one. That's the piece you have to claim yourself.

What Is the Medical Expense Deduction?

医療費控除 (iryōhi kōjo) lets you subtract part of a year's medical spending from your taxable income. Less taxable income means less tax — so what actually comes back is the tax you overpaid, not the medical costs themselves.

The amount you can deduct is worked out like this:

So the first 100,000 yen of medical spending is a floor you don't get to count (for most people). Everything above it becomes a deduction. The tax you get back is that deduction multiplied by your income tax rate — for many employees that's roughly 10–20%, and it also lowers your resident tax (住民税, jūminzei) for the following year.

Why the Childbirth Year Is Different

In a normal year, most healthy people don't spend 100,000 yen on medical care, so there's nothing to deduct and no reason to file. The year you have a baby is the exception. Between monthly prenatal checkups, the delivery and hospital stay, and the extra clinic visits that come with pregnancy, medical spending in that one year adds up fast — often well past the 100,000-yen floor even after the childbirth grant is subtracted.

That's why, even if you've never filed a tax return in Japan and never expect to again, the childbirth year is the one worth stopping for. It's also worth checking the year before and after, if pregnancy or fertility treatment spread your costs across more than one calendar year.

What Counts, and What Doesn't

The deduction is for actual medical care, which is broader than you might expect but does have clear edges. Based on the National Tax Agency's own examples for childbirth:

Subtract What You Got Back First

This is the step people get wrong, so it's worth being clear. Any money you received specifically to cover a medical cost has to be subtracted from that cost before you calculate the deduction. For childbirth, that means:

• The 出産育児一時金 (childbirth lump-sum grant, normally 500,000 yen) — subtracted from your delivery costs. See our childbirth grant guide.
• Any 高額療養費 (high-cost medical care refund) you received — see our high-cost medical care guide.
• Any payout from private medical insurance tied to a specific treatment or hospital stay.

One more detail: you only subtract a reimbursement from the specific cost it was paid for. If the childbirth grant is larger than your delivery costs, the leftover isn't subtracted from your other medical spending (say, a family member's dental work) — it stays with the delivery.

Combining the Whole Family's Costs

You don't count only your own medical bills. You can add together everything paid for yourself and for family members who 生計を一にする (share your household finances) — a spouse, children, and often parents you support, whether or not they live under the same roof. All of it goes on one person's return.

Because the refund scales with the filer's tax rate, it's usually best for the higher earner in the household to claim the whole family's costs. The main exception is when one spouse's income is under about 2 million yen: for them the floor is 5% of income rather than a flat 100,000 yen, which can occasionally work out better. If it's close, it's worth calculating both ways.

How to Actually File

Filing has become fairly manageable, and you don't hand in a shoebox of receipts anymore. The process:

1. Total up the year's medical costs for the whole household, and note any reimbursements to subtract.
2. Fill in the 医療費控除の明細書 (iryōhi kōjo no meisaisho — a medical expense statement). You summarize the costs on this form; you no longer submit the receipts themselves. If your health insurer sent a 医療費のお知らせ (a medical cost notice), you can use its total instead of listing every visit.
3. File the return. The easiest route is the National Tax Agency's online 確定申告書等作成コーナー (tax-return preparation site) and e-Tax. If you link マイナポータル (the My Number portal), a lot of your medical cost data can be pulled in automatically.
4. Keep your receipts for five years. You don't send them in, but the tax office can ask to see them, so hold on to the receipts and any medical cost notice.

One last thing: there's a separate, smaller scheme called the セルフメディケーション税制 (self-medication tax system) for over-the-counter medicine, and you can use only one of the two in a given year. For a childbirth year, the regular medical expense deduction is almost always the bigger one, so most families won't need to think about the alternative.

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