Final Tax Return: Who Files, When, e-Tax / Refund / Tax Manager
Employees with year-end adjustment usually don't file, but ¥200,000+ side income, ¥100,000+ medical expenses, 6+ Furusato Nozei, mid-year resignation, or pre-departure settlement require filing. e-Tax with My Number card in 30 minutes, paper postmark = filing day, refund typically arrives 3-6 weeks.
Final Tax Return (kakutei shinkoku) recalculates January 1 to December 31 income, deductions, and prior tax withholdings, and reports them to the local tax office. Income tax filing is usually from February 16 to March 15 of the following year (postponed for weekends/holidays; check the National Tax Agency for the year’s official announcement). Company employees with one salary source are usually handled by year-end adjustment and don’t need to file. But side income, medical expenses, Furusato Nozei (hometown tax donation), mid-year resignation, or pre-departure settlement requires per-NTA-condition judgment. This article splits it into 5 stages: judging → documents → submission → resignation/move/return-home → preservation, with concrete deadlines and amounts.
1. Start with the source-deduction certificate
The Source-Deduction Certificate (gensen-choshu-hyo) is the most basic document. It lists payment amount, post-deduction salary, deduction total, withholding tax, and company name. December-active employees are usually issued post-year-end-adjustment; mid-year resignees should request it from the prior company too (per Income Tax Act Article 226, issuance within 1 month of resignation is the company’s duty).
After receiving, verify: name, address, My Number submission status, dependent count, insurance deductions. Address errors propagate through tax office → residence tax notice → municipal records; people who resigned and moved in 2026 especially need to confirm the prior company’s mailing address.
Cases needing 2+ certificates: mid-year job change (prior + current employer), side income from a second salary source, post-resignation re-employment. All certificates must be summed for joint income calculation.
Sources: NTA No.7411: Issuance of Source-Deduction Certificate, Income Tax Act Article 226.
2. Six typical cases requiring filing
Company employees should file in these 6 typical cases:
| Case | Criterion | Notes |
|---|---|---|
| Annual income exceeds ¥20,000,000 | All file | Regardless of industry |
| Non-salary income exceeds ¥200,000 | Including writing fees, contract work, freelance, stock gains, crypto gains, real estate | ¥200,000 or less exempt for income tax (residence tax still requires filing at ward office) |
| Two+ salary sources and year-end-non-adjusted salary exceeds ¥200,000 | Including side jobs, temporary salary | |
| Resigned mid-year, didn’t re-employ within the year | Year-end adjustment not done | Filing usually yields a refund |
| Medical expense deduction | Annual paid medical expenses exceed ¥100,000 (or income’s 5% if income ¥2,000,000 or less) | Family aggregate possible |
| Furusato Nozei to 6+ municipalities | One-Stop Special doesn’t apply | Final filing also required |
Medical expense deduction calculation: deduction = paid medical expenses − insurance reimbursements − ¥100,000 (or income’s 5% if income ¥2,000,000 or less). Cosmetic, preventive, and ordinary supplements are excluded, but prescription medications, hospitals / pharmacies / dentistry / vision correction, fertility treatment, and outpatient travel (public transit only) are covered.
The One-Stop Special (Furusato Nozei without final filing) has conditions: ≤5 donation municipalities + no other filing requirements. 6+ municipalities or other filing reasons require including Furusato Nozei in the final filing.
Sources: NTA No.1900: Salary Earners Required to File, NTA No.1120: When You Pay Medical Expenses, MIC: Furusato Nozei One-Stop Special.
3. Documents and filing: e-Tax / paper / refund
Basic documents: source-deduction certificate, identity verification (My Number card or My Number notice + driver’s license), bank account (for refund deposit), deduction certificates (insurance, donations, medical bills), donation receipts (Furusato Nozei), residence card (foreigners).
Three submission methods:
| Method | Operation | Suits |
|---|---|---|
| e-Tax + My Number card | Smartphone NFC read, 30-60 min | My Number card + 4-digit PIN holder, fastest |
| e-Tax + ID/Password method | Get ID + password at tax office in advance (one-time, 5 min) | Without My Number card |
| Paper (mail / window) | Print at Final Tax Return Form Preparation Corner, postmark = filing day | Those uncomfortable with online |
e-Tax advantages: refunds typically arrive within 3 weeks (paper takes 4-6 weeks), deduction certificate attachment omitted, automated calculation. My Number card smartphone filing is the dominant method since 2024.
Payment methods (when tax is owed): direct deposit (account debit, late April lump sum), QR code (convenience store payment, ≤¥300,000), online banking, credit card (extra 0.7% fee), tax office window. Direct deposit is most convenient; just tick at filing.
Late filing penalties: late tax rate starts at 7.3% per year (2025 latest) + no-filing additional tax 5-20% (5% on self-reported, 15-20% after tax-office investigation).
Sources: NTA: Final Tax Return Form Preparation Corner, NTA: Filing Procedure / e-Tax, NTA No.9205: Late Tax.
4. Mid-year resignation / moving / return-home: 3 special cases
Mid-year resignation without re-employment: Year-end adjustment not done by the company, withholding tax has typically been over-withheld; filing usually yields a refund. Calculation: actual annual income + salary income deduction + basic deduction ¥480,000 + other deductions (social, life insurance, etc.) → correct income tax → the difference from withholding tax is the refund.
Moving: Filing location is judged by “address at time of filing.” Prior employer / municipality may send notices to the prior address; confirm postal forwarding (max 1 year free) is set up.
Pre-departure settlement (leaving Japan permanently) follows 3 steps: designate a Tax Manager (Tax Manager Notification form, choosing a representative from family, tax accountant, friend, or prior HR; submit before departure to local tax office); calculate unpaid residence tax at departure (residence tax based on prior year’s income, 12 months June through May; settle unpaid months proportionally); request the lump-sum withdrawal (pension; 6+ months of contribution lets foreigners apply within 2 years of departure for refund — 2 years is a hard deadline). Income tax and residence tax are separate systems; finishing one doesn’t automatically finish the other. Starting these 3 steps 3 months pre-departure is the safe plan.
Sources: NTA No.1923: Overseas Assignment and Tax Manager, JPS: Lump-Sum Withdrawal Request, MIC: Residence Tax Payment Obligation.
5. How long to keep records and where to ask
Filing copies, e-Tax receipt notices, payment receipts, refund notices, source-deduction certificates, medical receipts, and donation receipts should be kept by year. Legal requirement: blue-return filers 7 years, white-return filers 5 years. Company employees’ source-deduction certificates have no strict obligation, but next visa renewal, loan, rental, nursery application, and income proof commonly request 1-3 years of tax records. 5 years is a safe baseline.
Where to consult when uncertain: NTA web judgment flow has case-by-case judgment; phone consultation center (0570-00-5901, weekdays 8:30-17:00); nationwide 510 tax office windows (during 2-3 March filing period, reservation priority); tax accountants (individual cases ¥30,000-100,000, complex cases ¥100,000-300,000). “This is exempt” claims on social media are meaningless; tax decisions depend on the combination of income type, amount, residency status, withholding tax, and deduction items.
Sources: NTA: Bookkeeping / Records Preservation, NTA: Tax Consultation Service.
6. Common mistakes
Assuming side income ¥200,000 or less is fully exempt. Income tax is exempt, but residence tax filing at the municipal office is required (no ¥200,000 exemption for residence tax). Missing it can result in back-charging and potential underreporting.
Calculating medical expense deduction per individual. Correct approach is family aggregation (same household, including non-co-resident dependent children). The ¥100,000 annual threshold is per-aggregation; per-individual calculation may miss it.
Using the One-Stop Special for all donations within 5 municipalities. If you have other filing reasons (medical expenses, etc.), One-Stop doesn’t apply; Furusato Nozei must also be in the final filing. Otherwise the donation deduction is voided and refund is zero.
Not receiving source-deduction certificate after resignation. Income Tax Act Article 226 requires issuance within 1 month of resignation. If not received, demand it from the prior employer; otherwise the mid-year resignation refund is lost.
Pre-departure only designating Tax Manager, ignoring residence tax. Residence tax based on prior year’s income, with departure-day proportional settlement. Non-payment incurs late charges (7.3% per year) + impact on future re-entry “Tax Status Certificate.”
Believing all the “this is exempt” claims on social media. Each person’s combination of income type, amount, residency status, withholding tax, and deductions differs; NTA web judgment, tax accountant, or tax office confirmation is the safe approach.
Japanese key terms
- 確定申告 (kakutei shinkoku, Final Tax Return)
- 源泉徴収票 (gensen-choshu-hyo, Source-Deduction Certificate)
- 年末調整 (nenmatsu-chosei, year-end adjustment)
- 医療費控除 / ふるさと納税ワンストップ特例 (Medical Expense Deduction / Furusato Nozei One-Stop Special)
- e-Tax / マイナポータル連携
- 納税管理人 (nozei-kanrijin, Tax Manager)