"You can't get the medical expense deduction unless your medical costs exceed ¥100,000." Have you heard this?
"Exactly ¥100,000 won't do, and only the part above it comes back." "It's best to file all at once after the new year begins." These claims spread together, and half of them are true, while half are wrong depending on the person.
We checked this rumor against the original text of the Income Tax Act and the official information published by the National Tax Agency (NTA).
> **Four tax terms to know first**
>
> Here are plain-language explanations of the terms used in this article.
> - Medical expense deduction (iryōhi kōjo) = A system that lets you subtract, from your income, the part of the medical costs you paid from January 1 to December 31 of the year that exceeds a certain amount. Subtracting it lowers your tax.
> - Total amount of income (sōshotoku kingaku tō) = The total of your income for the year. It is the money you received (revenue) minus necessary expenses, so it is close to your "profit."
> - Refund return (kanpu shinkoku) = A final tax return filed to get back tax you overpaid. People who have no obligation to file can also use it.
> - Threshold (the cut-off amount) = The part of your medical costs that is subtracted in calculating the deduction. For some people it is ¥100,000, and for others it is 5% of their total amount of income.
## Conclusion
"You can't get it unless your medical costs exceed ¥100,000" is the rule for people whose total amount of income is ¥2,000,000 or more. For people whose total amount of income is under ¥2,000,000, the threshold is not ¥100,000 but "5% of the total amount of income."［1］［2］
"Only the part above the threshold is deducted" is true. Take your total medical costs and subtract the threshold (¥100,000, or the amount equal to 5% of the total amount of income) and any amounts reimbursed by insurance and the like; what remains is the deduction. The upper limit is ¥2,000,000.［1］［2］
If you mostly buy over-the-counter drugs, there is another option, the self-medication tax system (serufu medikēshon zeisei). Its threshold is ¥12,000 and its upper limit is ¥88,000, and you choose either it or the regular medical expense deduction, not both.［4］［5］
"File all at once after the new year begins" is also true. The medical expense deduction cannot be received through the year-end adjustment, so you claim it with a refund return. You can file for five years from January 1 of the year after the year in which you paid the costs.［2］［6］ And "if it is ¥100,000 or less, filing is a waste" is an assumption. People whose income is under ¥2,000,000 and people who buy many over-the-counter drugs can receive a deduction even at ¥100,000 or less.
Our verdict: "**Half true**." The figure "¥100,000" and the part about filing being a waste are wrong, while "only the part above the threshold comes back" and "file after the new year begins" are true.
## What the "¥100,000" really is
First, let's look at the original text of the law. The medical expense deduction is written in the Income Tax Act, Article 73, paragraph 1 (e-Gov Law Search).
> 居住者が、各年において、自己又は自己と生計を一にする配偶者その他の親族に係る医療費を支払つた場合において、その年中に支払つた当該医療費の金額（保険金、損害賠償金その他これらに類するものにより補てんされる部分の金額を除く。）の合計額がその居住者のその年分の総所得金額、退職所得金額及び山林所得金額の合計額の百分の五に相当する金額（当該金額が十万円を超える場合には、十万円）を超えるときは、その超える部分の金額（当該金額が二百万円を超える場合には、二百万円）を、その居住者のその年分の総所得金額、退職所得金額又は山林所得金額から控除する。[［1］](#ref-1)
>
> Reference translation (unofficial): Where a resident has paid, in a given year, medical expenses relating to the resident or to a spouse or other relative with whom the resident shares a livelihood, and the total amount of those medical expenses paid during that year (excluding the portion reimbursed by insurance money, damages or the like) exceeds an amount equal to 5% of the total of the resident's total income amount, retirement income amount and timber income amount for that year (or ¥100,000, if that amount exceeds ¥100,000), the amount of the excess (or ¥2,000,000, if that amount exceeds ¥2,000,000) is deducted from the resident's total income amount, retirement income amount or timber income amount for that year.
This is a rather stiff sentence, so here is what it means. The provision works in the following three steps.
1. Calculate the threshold. Work out the amount equal to 5% of the total amount of income. If it exceeds ¥100,000, the threshold switches to ¥100,000.
2. If your total medical costs (excluding the part reimbursed by insurance and the like) exceed the threshold, the excess is your deduction.
3. The upper limit of the deduction is ¥2,000,000.
In other words, "¥100,000" is a cap on the threshold for people whose 5% amount exceeds ¥100,000. In Tax Answer No.1120, the NTA explains the same thing as follows.
> （注）その年の総所得金額等が200万円未満の人は、総所得金額等の5パーセントの金額[［2］](#ref-2)
>
> Reference translation (unofficial): (Note) For a person whose total amount of income, etc. for the year is under ¥2,000,000, the amount equal to 5% of the total amount of income, etc.
5% of the total amount of income becomes ¥100,000 exactly when the total amount of income is ¥2,000,000. So you can remember it simply as: "if your total amount of income is under ¥2,000,000, the threshold is 5%; if it is ¥2,000,000 or more, the threshold is ¥100,000."
## People who can claim it with less than ¥100,000
Let's compare two people to see why "it's absolutely no good unless you exceed ¥100,000" is wrong. Both had ¥90,000 of medical costs for the year (with nothing reimbursed by insurance and the like).
| Person | Total amount of income | Threshold | Medical expense deduction |
| --- | --- | --- | --- |
| A (company employee) | ¥3,500,000 | ¥100,000 (5% is ¥175,000, so it switches to the cap) | Zero (¥90,000 is below the threshold) |
| B (pension only) | ¥1,500,000 | ¥75,000 (¥1,500,000 × 5%) | ¥15,000 (¥90,000 − ¥75,000) |
Both people have the same ¥90,000 of medical costs. Even so, B is allowed a medical expense deduction of ¥15,000. B's medical costs do not reach ¥100,000, but because B's threshold is not ¥100,000, B can claim the deduction.
What makes this difference is the "total amount of income." The 5% standard works in your favor in years when your earnings are low, the year you retire and live on a pension only, or a year when your business ran at a loss. If you remember only the figure ¥100,000 and give up, you throw away a deduction you were entitled to.
Now back to the rumor "if it is ¥100,000 or less, filing is a waste." This statement has two errors. The first is that people whose total amount of income is under ¥2,000,000 can get a deduction even with medical costs of ¥100,000 or less. The second is that, even for people whose deduction comes to zero, filing itself is not a loss. Your tax burden does not increase. When the deduction is zero, no tax comes back. Also, for people who often buy over-the-counter drugs, there is a separate special rule, the self-medication tax system.
Note that this is not about gathering every last yen of medical costs. The "money that gets subtracted," which we look at in the next section, has a larger effect on the amount.
## Pitfall 1: Two kinds of money are subtracted
The part "only the part above the threshold comes back" is true, as described. Two kinds of money are subtracted from your total medical costs.
The first is amounts reimbursed by insurance and the like. In Tax Answer No.1120, the NTA explains that the amount eligible for the medical expense deduction is calculated with the following formula.
> （実際に支払った医療費の合計額-（1）の金額）-（2）の金額[［2］](#ref-2)
>
> Reference translation (unofficial): (Total medical expenses actually paid − the amount in (1)) − the amount in (2)
> （例） 生命保険契約などで支給される入院費給付金や健康保険などで支給される高額療養費・家族療養費・出産育児一時金など[［2］](#ref-2)
>
> Reference translation (unofficial): (Examples) Hospitalization benefits paid under life insurance contracts and the like, and high-cost medical care benefits, family medical care benefits, lump-sum childbirth and child-rearing allowances and the like paid under health insurance and the like.
The second is the amount in (2), which is the threshold (¥100,000, or the amount equal to 5% of the total amount of income).
Let's calculate with a concrete example. A person whose total amount of income is ¥3,000,000 pays ¥280,000 in medical costs during the year and receives ¥100,000 in hospitalization benefits.
- ¥280,000 medical costs − ¥100,000 hospitalization benefits = ¥180,000
- ¥180,000 − ¥100,000 threshold = ¥80,000 (the medical expense deduction)
Of the ¥180,000 you paid out of pocket, ¥80,000 becomes the deduction. This "only the part above" feeling is just as the rumor says.
There is one point to note. Insurance money is subtracted only up to the amount of the medical costs it was paid for. Even if some benefit is left over, it is not subtracted from your other medical costs[［2］](#ref-2).
## Pitfall 2: What is not counted as medical costs
Another pitfall is that "not everything you paid counts as medical costs." The Income Tax Act, Article 73, paragraph 2 sets out the scope of medical costs as follows.
> 前項に規定する医療費とは、医師又は歯科医師による診療又は治療、治療又は療養に必要な医薬品の購入その他医療又はこれに関連する人的役務の提供の対価のうち通常必要であると認められるものとして政令で定めるものをいう。[［1］](#ref-1)
>
> Reference translation (unofficial): "Medical expenses" as referred to in the preceding paragraph means those consideration amounts prescribed by Cabinet Order as being recognized as ordinarily necessary, among the consideration for medical examination or treatment by a physician or dentist, the purchase of medicines necessary for treatment or recuperation, and other medical care or the provision of personal services related to it.
It is limited to what is "recognized as ordinarily necessary." In Tax Answer No.1122, the NTA shows with concrete examples what is covered and what is not[［3］](#ref-3).
| Covered (examples) | Not covered (examples) |
| --- | --- |
| Payment for examination or treatment by a physician or dentist | Health checkup fees and gift money (generally not covered) |
| The cost of medicines needed for treatment | Medicines such as vitamin supplements taken to prevent illness or promote health |
| Costs of traveling to the hospital (train, bus, etc.) | Gasoline and parking fees for a private car |
| Purchase costs of artificial arms and legs, crutches, hearing aids and the like that are directly necessary for examination or treatment by a physician, etc.[［3］](#ref-3) | Massage to relieve tiredness |
If you add items that are not covered to your medical costs and wrongly think "I passed ¥100,000," the deduction may be denied even though you filed. When you put your receipts together, sorting them with this table gives you peace of mind.
## File after the new year begins
The medical expense deduction cannot be received through the year-end adjustment. You must submit a return yourself. A refund return is the procedure by which people with no obligation to file get back tax they overpaid. People who left their company partway through the year can also use a refund return[［6］](#ref-6).
> 還付申告書は、確定申告期間とは関係なく、その年の翌年1月1日から5年間提出することができます。[［6］](#ref-6)
>
> Reference translation (unofficial): A refund return can be submitted for five years from January 1 of the year following that year, regardless of the final tax return filing period.
The part of the rumor that says "it's best to file all at once after the new year begins" is correct knowledge. However, there is a five-year deadline. If you leave it alone, the statute of limitations will prevent you from receiving the refund.
## If you mainly buy over-the-counter drugs: the self-medication tax system
If your medical costs are mostly over-the-counter drugs, there is a system to consider before the regular medical expense deduction: the self-medication tax system. It is a special rule within the medical expense deduction, and it applies to people who are taking "certain measures" to maintain and improve their health and prevent disease (health checkups, vaccinations, regular health checkups at their workplace, and the like)[［4］](#ref-4).
The deduction is the purchase cost of eligible over-the-counter drugs (such as switch OTC drugs) minus ¥12,000, with an upper limit of ¥88,000[［4］](#ref-4). Because the cut-off is a low ¥12,000, you can easily reach the threshold even in a year with almost no medical costs.
This special rule has a time limit. It covers purchases made up to December 31, 2026 (Reiwa 8). From 2027 on, it depends on tax reform[［7］](#ref-7).
| Item | Regular medical expense deduction | Self-medication tax system |
| --- | --- | --- |
| Threshold | ¥100,000, or 5% of the total amount of income | ¥12,000 |
| Upper limit of deduction | ¥2,000,000 | ¥88,000 |
| Eligible costs | Medical costs for treatment in general | Purchase costs of specified over-the-counter drugs and the like |
| Conditions | None | "Certain measures" are required |
The two are alternatives, and you cannot receive both[［5］](#ref-5). As a rule of thumb, the regular medical expense deduction suits a year with large hospital treatment costs, and the self-medication tax system suits people who buy over-the-counter drugs such as cold medicine and eye drops throughout the year. Which is better depends on the breakdown, so calculate both amounts and compare them before you file. You make the choice when you file, and you cannot change it afterward by a request for correction or an amended return[［5］](#ref-5).
## What to do
Here are the things to do after the new year begins, in three steps.
### Step 1: Add up your medical costs
- Count only what you paid from January 1 to December 31. Unpaid amounts count as medical costs of the year in which you actually pay them.
- Make a note of the amounts reimbursed by insurance and the like. High-cost medical care benefits and lump-sum childbirth and child-rearing allowances are included.
- Leave out costs that are not covered (health checkups, vitamin supplements for prevention, gasoline for a private car, and the like).
### Step 2: Calculate the threshold and the deduction
Total amount of income
Threshold
Under ¥2,000,000
The amount equal to 5% of the total amount of income
¥2,000,000 or more
¥100,000
Calculate the deduction as total medical costs − amounts reimbursed by insurance and the like − the threshold. The upper limit is ¥2,000,000.
### Step 3: Choose how to file
- People who have an obligation to file (such as the self-employed) include the medical expense deduction in their final tax return.
- People with no obligation to file (such as company employees whose year-end adjustment is done) file a refund return. You can submit it at any time for five years from January 1 of the year after the year in which you paid the costs.
- If your costs are mainly over-the-counter drugs, calculate which is better, the self-medication tax system or the regular deduction, and then choose. You cannot change your choice.
When you file, you attach the "Statement of medical expenses (iryōhi kōjo no meisaisho)" to your final tax return. You no longer need to attach the receipts themselves, but keep them for five years from the filing deadline and so on, so that you can show them if the tax office asks.
## Summary
"You can't get the medical expense deduction unless you exceed ¥100,000" is half true. ¥100,000 is the threshold only for people whose total amount of income is ¥2,000,000 or more. If it is under ¥2,000,000, the threshold is 5% of the total amount of income, and you can get the deduction even with medical costs under ¥100,000. "Only the part above comes back" is true: the deduction is what remains after subtracting the threshold and amounts reimbursed by insurance and the like. You claim it not through the year-end adjustment but with a refund return after the new year begins (five years). In a year when you mainly buy over-the-counter drugs, the self-medication tax system with its ¥12,000 threshold is an option.
For tax rules you have memorized as a number, we recommend checking again "who that number applies to." The ¥100,000 for the medical expense deduction turned out to be a figure that fits people in better circumstances.
---
### Sources
- ［1］[Income Tax Act, Article 73 (e-Gov Law Search, Japanese)](https://laws.e-gov.go.jp/law/340AC0000000033/article/73) Checked: 2026-10-05
- ［2］[NTA Tax Answer No.1120 "When you have paid medical expenses (medical expense deduction)" (Japanese)](https://www.nta.go.jp/taxes/shiraberu/taxanswer/shotoku/1120.htm) Checked: 2026-10-05
- ［3］[NTA Tax Answer No.1122 "Medical expenses eligible for the medical expense deduction" (Japanese)](https://www.nta.go.jp/taxes/shiraberu/taxanswer/shotoku/1122.htm) Checked: 2026-10-05
- ［4］[NTA Tax Answer No.1129 "When you have paid for the purchase of specified over-the-counter drugs, etc. (special rule for the medical expense deduction) [self-medication tax system]" (Japanese)](https://www.nta.go.jp/taxes/shiraberu/taxanswer/shotoku/1129.htm) Checked: 2026-10-05
- ［5］[NTA Tax Answer No.1131 "Choosing between the self-medication tax system and the regular medical expense deduction" (Japanese)](https://www.nta.go.jp/taxes/shiraberu/taxanswer/shotoku/1131.htm) Checked: 2026-10-05
- ［6］[NTA Tax Answer No.2030 "Refund return" (Japanese)](https://www.nta.go.jp/taxes/shiraberu/taxanswer/shotoku/2030.htm) Checked: 2026-10-05
- ［7］[Act on Special Measures Concerning Taxation, Article 41-17 (e-Gov Law Search, Japanese)](https://laws.e-gov.go.jp/law/332AC0000000026/article/41-17) Checked: 2026-10-05
Note: This article is based on laws and official information as of October 5, 2026. It is a translation of the Japanese original; if the two differ, the Japanese version prevails. Quotations from laws and official sources are given in the original Japanese, followed by unofficial reference translations. Sources are limited to laws (e-Gov) and official NTA pages, all in Japanese. If a correction is needed after publication, a correction record will be added at the end of this article ([Correction policy](/en/methodology/)).