Is it true that "you can use it for either the medical expense deduction or the self-medication tax system"?

During tax filing season, you may see the explanation that “pharmacy receipts can be used for either the medical expense deduction or the self-medication tax system.” This explanation is mostly correct, because you can choose one of the two and use it. However, there are three conditions. You can use only one of them in the same year. After you file, you cannot choose again. And you can use the self-medication tax system only if you bought eligible medicines and you yourself have had a health checkup or a similar measure.

To begin with, these two are not separate deductions. The self-medication tax system is a special rule that replaces part of the calculation formula of the medical expense deduction. The provision says “at the person’s choice” (「その者の選択により」), and using both at the same time is not allowed. If you choose one, you cannot use the other. If you misunderstand this point, the amount of your deduction changes.

Five tax terms, explained first

Here are plain-language explanations of the terms used in this article.

• Medical expense deduction (iryōhi kōjo) = a system that lets you subtract an amount from your income when the medical expenses you paid in a year exceed a certain amount
• Self-medication tax system (serufu-medikēshon zeisei) = a special rule that lets you subtract the cost of over-the-counter medicines using the formula of the medical expense deduction
• Specified OTC drug purchase costs (tokutei ippan-yō iyakuhin-tō kōnyūhi) = the cost of buying over-the-counter medicines (such as switch OTC drugs) covered by this special rule
• Switch OTC drugs = medicines that were switched from doctor’s prescription drugs to drugs you can buy at a pharmacy
• Certain health measures (ittei no torikumi) = health activities such as health checkups, vaccinations and cancer screenings that this special rule requires

Conclusion

The verdict is TRUE, with conditions. You can choose one of the two and use it. However, you cannot use both in the same year, and you cannot choose again after filing. Before you file, calculate both amounts and compare them.

The two systems come from one provision

First, let’s check how the system works. The regular medical expense deduction is in Article 73 of the Income Tax Act.

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］

(Income Tax Act, Article 73, paragraph 1. The quotation is in the original Japanese.)［1］

Put plainly, it says this. From the total medical expenses you paid in a year, subtract ¥100,000 (or 5% of total income, etc. for people whose total income, etc. is under ¥2 million). The remaining amount can be subtracted from your income. The deduction is capped at ¥2 million.

Next, let’s look at the provision for the self-medication tax system: Article 41-17 of the Act on Special Measures Concerning Taxation. The provision currently in force (the version covering payments made up to December 31, 2026) reads as follows.

居住者が平成二十九年一月一日から令和八年十二月三十一日までの間に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特定一般用医薬品等購入費を支払つた場合において当該居住者がその年中に健康の保持増進及び疾病の予防への取組として政令で定める取組を行つているときにおけるその年分の所得税法第七十三条第三項に規定する医療費控除については、その者の選択により、 ［2］

(Act on Special Measures Concerning Taxation, Article 41-17, paragraph 1. Excerpt. The quotation is in the original Japanese.)［2］

This provision does not create a new deduction. It sets out how the medical expense deduction (Income Tax Act, Article 73) is to be read differently. It is a mechanism that applies eligible medicine costs to the same formula as medical expenses.

The latter part of the same provision replaces the figures. The ¥100,000 floor becomes ¥12,000, and the ¥2 million cap becomes ¥88,000.

The two use the same formula. The only differences are the amounts you put in and the floor and cap. For that reason, you cannot use both in the same year.

“Selective application” is written both in the provision and by the NTA

Regarding the provision’s “at the person’s choice,” the NTA explains it as follows in Tax Answer No.1131.

セルフメディケーション税制は医療費控除の特例であり、通常の医療費控除との選択適用となりますので、いずれか一方を選択して適用することになります。 ［3］

(NTA Tax Answer "No.1131 Selective application of the self-medication tax system and the regular medical expense deduction." The quotation is in the original Japanese.)［3］

The same page has a sentence that is easy to overlook. It covers the case where medical expenses other than medicines are large.

また、セルフメディケーション税制の適用を受ける場合には、この特例の対象となる特定一般用医薬品等購入費以外の医療費の額が通常の医療費控除の適用下限額（10万円と総所得金額等の5パーセント相当額のいずれか低い方の金額）を超える場合であっても、通常の医療費控除を併せて受けることはできません。 ［3］

(NTA Tax Answer "No.1131." The quotation is in the original Japanese.)［3］

For example, consider a year in which you spent ¥30,000 on medicines and paid ¥200,000 at hospital counters. Your medical expenses other than medicines are ¥200,000, which exceeds ¥100,000. Even so, if you choose the self-medication tax system, you cannot take the regular medical expense deduction. You cannot add the two figures together and file.

This is where a common misunderstanding arises: “Medical expenses that are not eligible should be deductible separately.” The provision and the NTA’s explanation reject that idea. For the medical expense deduction for a given year, you can choose only one of the two.

Once you choose, you cannot change

After you file, you cannot choose again. The NTA writes the following.

（注）セルフメディケーション税制の適用を受けることを選択して確定申告書を提出した場合には、その後において納税者が更正の請求や修正申告書により、セルフメディケーション税制から通常の医療費控除へ適用を変更することはできません。同様に通常の医療費控除を受けることを選択した場合も変更できません。 ［3］

(NTA Tax Answer "No.1131." The quotation is in the original Japanese.)［3］

A request for correction is a procedure for having your tax corrected to the right amount, for example when you paid too much. An amended return is a procedure for correcting your return in the direction of increasing the tax you pay. Neither procedure lets you change the system you chose. The only way is to compare the amounts and decide before you submit your return.

Which is better depends on how much you spend on medicines

To compare, you simply put the two formulas side by side. Both subtract a floor from the eligible amount. The table shows examples for people whose total income, etc. is ¥2 million or more (floor of ¥100,000). For people under ¥2 million, the floor is 5% of total income, etc.

Row 1 is a year in which total medical expenses do not reach ¥100,000. The regular medical expense deduction is ¥0. With the self-medication tax system, you can subtract ¥18,000. In this case, the special rule is better.

Row 2 is a year with large hospital expenses. The regular medical expense deduction is ¥120,000, and the special rule gives ¥8,000. The difference is large, so you choose the regular medical expense deduction.

Row 3 is a year with large medicine costs. The deduction under the special rule stops at ¥88,000. Even if medicine costs exceed ¥100,000, it does not increase any further, because the cap in the provision is ¥88,000.

The regular medical expense deduction column in the table includes the eligible medicine costs. If those medicine costs are payment for medicines necessary for treatment or medical care, they also count as medical expenses for the regular medical expense deduction. ［9］

The NTA explains the self-medication tax system’s formula as follows.

健康の保持増進および疾病の予防への取組として一定の健康診断や予防接種などを行っている方が、自己または自己と生計を一にする配偶者やその他の親族の特定一般用医薬品等購入費を支払った場合には、通常の医療費控除との選択により、その年中の特定一般用医薬品等購入費の合計額（保険金等により補填される部分の金額を除きます。）のうち、12,000円を超える部分の金額（88,000円を限度）を控除額とする ［4］

(NTA Tax Answer "No.1120 When you pay medical expenses (medical expense deduction)." The quotation is in the original Japanese.)［4］

Here too it says “at your choice between this and the regular medical expense deduction” (「通常の医療費控除との選択により」). Even in the explanation of the formula, it is assumed that you choose one and use it.

Who can use it, and which medicines

The self-medication tax system has two conditions that the regular medical expense deduction does not: health measures and the type of medicine.

Health measures include health checkups, municipal cancer screenings, vaccinations, regular health checkups at work, and specified health checkups and specified health guidance. The person filing the return must be the one who carried out these measures.

なお、申告される方が「一定の取組」を行っている必要があります（申告される方と生計を一にする配偶者その他の親族の方が「一定の取組」を行っている必要はありません。）。 ［5］

(NTA Tax Answer "No.1129." The quotation is in the original Japanese.)［5］

You can add up your family members’ medicine costs, but a health checkup taken by a family member does not meet the condition.

The cost of the health measures themselves is not eligible for this special rule’s deduction. The same applies to your out-of-pocket cost for a comprehensive medical checkup (ningen dokku).

「一定の取組」に要した費用は控除の対象となりません。 ［9］

(NTA "What is the self-medication tax system." The quotation is in the original Japanese.)［9］

The medicines are switch OTC drugs and similar medicines, which were switched from doctor’s prescription drugs to drugs you can buy at a pharmacy. Whether a medicine is eligible is shown on the receipt. You can also check the list of eligible products published by the Ministry of Health, Labour and Welfare (MHLW).

The scope of eligible medicines was revised for purchases made on or after January 1, 2026.

次の医薬品のうち、医療用薬剤との代替性が特に高いもの（令和8年1月1日以降に購入したものについては、その使用による医療保険療養給付費の適正化の効果が低いと認められる医薬品を除く。）として厚生労働大臣が財務大臣と協議して定めるもの ［6］

(NTA Tax Answer "No.1132." Excerpt. The quotation is in the original Japanese.)［6］

In other words, medicines found to have a low effect have been excluded for purchases made on or after January 1, 2026. A medicine that was eligible last year may no longer be eligible this year. Check the product list for the year you bought it.

Eligible medicine costs may also be eligible for the regular medical expense deduction.

セルフメディケーション税制の対象となる医薬品の購入費用であるもののうち、それが治療や療養に必要な医薬品の購入の対価であるものについては、通常の医療費控除を受けることを選択した場合の控除の対象となる医療費にも該当します。 ［9］

(NTA "What is the self-medication tax system." The quotation is in the original Japanese.)［9］

The same receipt can be eligible under either system. However, you can use only one of them in the same year. The NTA sentence above does not mean “you can use it for either one as you like.” You cannot put the same medicine costs into both calculations.

From January 1, 2027, the time limit changes and coverage expands

The self-medication tax system has an application period. The provision currently in force sets the payment period as follows.

居住者が平成二十九年一月一日から令和八年十二月三十一日までの間に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特定一般用医薬品等購入費を支払つた場合 ［2］

(Act on Special Measures Concerning Taxation, Article 41-17, paragraph 1. Excerpt. The quotation is in the original Japanese.)［2］

Under the current provision, payments made up to December 31, 2026 are covered. You can use it under this provision when you file for 2026 (from February to March 2027). The NTA’s No.1132 also sets the purchase period as “from January 1, 2022 to December 31, 2026” (「令和4年1月1日から令和8年12月31日まで」). ［6］

However, the system does not expire. The Act Partially Amending the Income Tax Act, etc. (Act No. 12 of 2026) takes effect on January 1, 2027, and Article 41-17, paragraph 1 changes to set the period separately for each category of medicine. The amended provision reads as follows.

一　次項第一号に掲げる医薬品（医薬品、医療機器等の品質、有効性及び安全性の確保等に関する法律第二条第一項に規定する医薬品をいう。次項において同じ。）である一般用医薬品等（薬局製造販売医薬品を除く。）に係る特定一般用医薬品等購入費　平成二十九年一月一日以後の期間

二　前号に掲げる特定一般用医薬品等購入費以外の特定一般用医薬品等購入費　平成二十九年一月一日から令和十三年十二月三十一日までの期間 ［10］

(Act on Special Measures Concerning Taxation, Article 41-17, paragraph 1 (as in force on January 1, 2027). Excerpt. The quotation is in the original Japanese.)［10］

Here is how to read it.

• For switch OTC drugs (excluding pharmacy-manufactured drugs), the time limit is removed. Payments made on or after January 1, 2017 remain covered.
• Other eligible medicines are covered for payments made up to December 31, 2031. From 2032, this group is no longer covered.
• OTC test kits (in vitro diagnostics) are added to the eligible medicines. MHLW Notice No. 307 of 2026 applies from January 1, 2027. ［11］ Test kits fall into the “other” group, so they are also covered only up to December 31, 2031.
• The amounts of ¥12,000 and ¥88,000, and the rule “at the person’s choice,” do not change after the amendment.

This part is easy to misread. The NTA’s Tax Answers are based on the laws as of April 1, 2026 (this is stated at the top of No.1133). For that reason, No.1132 appears to end at “December 31, 2026.” Check the amended content in the not-yet-effective version on e-Gov or in the MHLW’s PDF titled “After amendment [effective January 1, 2027]” (「改正後【令和9年1月1日施行】」).

Tax rules change with each year’s amendments. Before you file, check the provisions that apply to that year. The figures in this article may also change after the date checked.

Four common mistakes

The first is adding the same receipt to both totals. The statement of details for the medical expense deduction and the statement of details for the self-medication tax system are separate documents. If you prepare and submit both, your return deducts the same spending twice.

The second is including the cost of health checkups. The cost of the health measures themselves is not deductible. The health measures are a precondition for deducting medicine costs.

The third is counting a family member’s health measures as your own. You can add up family members’ medicine costs, but the health measures must be carried out by the person filing.

The fourth is thinking you will get the money back through the year-end adjustment. Both the medical expense deduction and this special rule are deductions you receive by filing a final tax return. The NTA describes how to file as follows.

医療費控除に関する事項その他の必要事項を記載等した確定申告書を提出してください。 ［4］

(NTA Tax Answer "No.1120." The quotation is in the original Japanese.)［4］

Neither the medical expense deduction nor the self-medication tax system can be received through your company’s year-end adjustment.

What to do

1. Gather a year’s medical expenses, and count the eligible medicine costs separately (identify them by the mark on the receipt)
2. Calculate the regular medical expense deduction (total medical expenses − ¥100,000; for people whose total income, etc. is under ¥2 million, subtract 5% of total income, etc.)
3. Calculate the self-medication tax system amount (eligible medicine costs − ¥12,000; cap of ¥88,000)
4. Compare 2 and 3, and choose the larger one
5. Attach only the one statement of details for the system you chose to your final tax return
6. Keep the receipts and the results notices for your health measures for five years from the filing deadline

Submit only the statement of details for the system you chose.

令和3年分以後のセルフメディケーション税制の適用に関する事項を記載した確定申告書を令和4年1月1日以後に提出する場合は、特定一般用医薬品等購入費の額や一定の取組に関する事項など定められた事項の記載のある明細書を確定申告書に添付してください。 ［8］

(NTA Tax Answer "No.1134." The quotation is in the original Japanese.)［8］

Documents proving your health measures no longer need to be attached to the return. However, until five years have passed from the filing deadline, the tax office may ask you to present or submit them.

上記の一定の取組を行ったことを明らかにする書類は、令和3年分以後のセルフメディケーション税制の適用に関する事項を記載した確定申告書を令和4年1月1日以後に提出する場合に、確定申告書への添付または提示は不要ですが、確定申告期限等から5年を経過する日までの間、税務署から提示または提出を求める場合があります。 ［8］

(NTA Tax Answer "No.1134." The quotation is in the original Japanese.)［8］

Summary

“Pharmacy receipts can be used for either the medical expense deduction or the self-medication tax system” is TRUE, with conditions. You can use only one of the two, because the self-medication tax system is a special rule that replaces the calculation formula of the medical expense deduction (Act on Special Measures Concerning Taxation, Article 41-17, paragraph 1, “at the person’s choice”; NTA No.1131). If you choose one, you cannot take the other, even if your other medical expenses exceed ¥100,000. You also cannot choose again after filing.

Which one to use depends on the amounts. In a year when total medical expenses do not reach ¥100,000 and eligible medicine costs exceed ¥12,000, the special rule is better. In a year with large hospital expenses, the regular medical expense deduction is better. Calculate both formulas before you prepare your return.

Under the current provision, payments made up to December 31, 2026 are covered. From January 1, 2027, the amended provision applies. The time limit is removed for switch OTC drugs (excluding pharmacy-manufactured drugs), and other eligible medicines are covered for payments made up to December 31, 2031. OTC test kits are also added. Before you file, check the provision that applies to that year.

出典

• ［1］所得税法第73条（医療費控除）— e-Gov法令検索　確認日：2026-10-28
• ［2］租税特別措置法第41条の17（特定一般用医薬品等購入費を支払つた場合の医療費控除の特例）— e-Gov法令検索　確認日：2026-10-28
• ［3］No.1131 セルフメディケーション税制と通常の医療費控除との選択適用— 国税庁　確認日：2026-10-28
• ［4］No.1120 医療費を支払ったとき（医療費控除）— 国税庁　確認日：2026-10-28
• ［5］No.1129 特定一般用医薬品等購入費を支払ったとき（医療費控除の特例）— 国税庁　確認日：2026-10-28
• ［6］No.1132 セルフメディケーション税制の対象となる特定一般用医薬品等購入費— 国税庁　確認日：2026-10-28
• ［7］No.1133 健康の保持増進及び疾病の予防への取組を行っている場合— 国税庁　確認日：2026-10-28
• ［8］No.1134 取組を行ったことを明らかにする書類の具体例— 国税庁　確認日：2026-10-28
• ［9］セルフメディケーション税制とは（確定申告特集）— 国税庁　確認日：2026-10-28
• ［10］租税特別措置法（昭和32年法律第26号）改正後【令和9年1月1日施行】— 厚生労働省（PDF）／同 令和9年1月1日施行版（未施行版）— e-Gov法令検索　確認日：2026-10-28
• ［11］令和8年厚生労働省告示第307号（租税特別措置法施行令第26条の27の3第4項）— 厚生労働省（PDF）　確認日：2026-10-28

Note: This article is based on laws and official information as of October 28, 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. Sources are based on laws (e-Gov) and official materials of the NTA and the MHLW, all in Japanese. If a correction is needed after publication, a correction record will be added at the end of this article (Correction policy).