How to Pay Your Taxes in Japan Step by Step

Paying taxes in Japan as a foreigner can feel overwhelming at first — forms in Japanese, unfamiliar systems, and tight deadlines. But once you understand the process, it is quite straightforward. This guide walks you through every step of paying your taxes in Japan, from understanding your residency status to filing online with e-Tax.

Whether you are a salaried employee, freelancer, or side-income earner, this step-by-step guide covers everything you need to know about the Japanese tax system for foreigners.

Step 1 — Determine Your Tax Residency Status

Before anything else, you need to know how Japan classifies you for tax purposes. Your residency status determines what income is taxed and at what rates.

Japan uses three residency categories:

Most long-term expats (working visa holders who have been in Japan for over a year) fall into the Non-Permanent Resident category. This is important because it determines whether your overseas income — like foreign bank interest or dividends — is subject to Japanese tax.

For a complete overview of tax obligations for foreigners, see The Complete Guide to Taxes in Japan for Foreigners.

Step 2 — Understand Japan's Income Tax Brackets

Japan uses a progressive income tax system for residents. National income tax rates range from 5% to 45%, and there is an additional 10% resident tax (住民税, juminzei) based on the previous year's income.

National Income Tax Brackets (2025)

Important: An additional Special Reconstruction Income Tax of 2.1% is applied on top of your national income tax. This surcharge continues through December 31, 2037, and was introduced to fund reconstruction after the 2011 earthquake and tsunami.

So if your national income tax is 20%, your effective rate is 20% × 1.021 = approximately 20.42%.

For the 2025 tax year, the basic exemption (kiso kojo) increased to ¥580,000, providing a slightly larger deduction than previous years.

Step 3 — Know if You Need to File a Tax Return (Kakutei Shinkoku)

Not everyone needs to file a kakutei shinkoku (確定申告, final income tax return). Many salaried employees at Japanese companies have their taxes handled automatically through the Year-End Adjustment (年末調整, nenmatsu chosei) done by their employer in December.

You DO need to file if you:

• Are self-employed or freelance
• Work for an overseas employer that doesn't do year-end adjustment
• Have multiple sources of income (e.g., two part-time jobs)
• Earn side income exceeding ¥20,000 per year (net after expenses)
• Have rental income, investment income, or overseas income
• Want to claim medical expense deductions (over ¥100,000)
• Made Furusato Nozei donations to more than 5 municipalities
• Are applying for a housing loan deduction for the first year

You generally DON'T need to file if you:

• Work at a single Japanese company that handles your year-end adjustment
• Have no significant side income or investment gains
• Don't need to claim special deductions

Even if the 20,000 yen threshold doesn't require national income tax filing, you may still be required to file for resident tax at your local city/ward office. Failing to do so can result in penalties of up to 14.6% annually.

Step 4 — Gather Your Documents

Before filing, collect the following documents:

Essential Documents

Additional Documents (if applicable)

• Medical expense receipts (領収書) if claiming deductions
• Donation receipts for Furusato Nozei (ふるさと納税寄附金受領証明書)
• Records of side income and business expenses
• Proof of overseas dependents (for overseas family support deductions)
• Blue tax registration certificate (if using ao-iro shinkoku)

Your gensen choshu hyo (withholding tax certificate) from your employer is the most critical document. It shows your total annual income, taxes withheld, and social insurance contributions paid.

For more on managing finances in Japan, see The Complete Guide to Banking and Finance in Japan.

Step 5 — Choose Your Filing Method

Japan offers three ways to file your tax return:

Option A: e-Tax (Online) — Recommended

e-Tax (国税電子申告・納税システム) is Japan's official online tax filing system. It is the fastest and most convenient method, especially with multi-language support added in recent years.

Advantages:

• File from home, 24 hours a day
• Available in English, Chinese, Vietnamese, Portuguese, and Nepali
• Refunds processed in approximately 3 weeks (vs. 1–2 months for paper)
• No need to attach documents
• Built-in automatic calculation reduces errors

How to use e-Tax:

1. Visit the National Tax Agency website and select "Kakutei Shinkoku" (確定申告)
2. Choose "Create Return" and follow the guided prompts
3. Enter your income, deductions, and My Number
4. Submit electronically using your My Number Card and a card reader, or via mobile

For a full walkthrough of the e-Tax filing process, check out this comprehensive guide on Living in Nihon.

Option B: Paper Filing by Mail

Download Form A (employees/pension income) or Form B (all income types) from the National Tax Agency website, fill them out, and mail to your local tax office before the deadline.

Disadvantages: Slower refunds (1–2 months), more difficult to check for errors, no automatic calculations.

Option C: In-Person at the Tax Office (Zeimusho)

Visit your local tax office (税務署, zeimusho) during the filing period. Staff can help you fill out your return, and some offices offer multilingual assistance. Be prepared to wait 2–4 hours during peak filing times.

Step 6 — File Your Return Before the Deadline

The tax filing deadline in Japan is March 15 each year (or March 16 when March 15 falls on a weekend). You are filing for income earned during the previous calendar year (January 1 – December 31).

2026 Filing Period

• Filing for: FY2025 income (January 1 – December 31, 2025)
• Period: February 16, 2026 – March 16, 2026
• Deadline for payments: March 15, 2026

If you miss the March 15 deadline:

• A late filing penalty applies (usually 5% of unpaid tax)
• Late payment interest of up to 14.6% per year accrues from the original due date
• It may also affect your visa renewal in some cases

If you cannot meet the deadline due to illness, disaster, or unavoidable circumstances, you may apply for an extension at your local tax office.

For more on life administration as a foreigner, visit The Complete Guide to Daily Life in Japan for Foreigners.

Step 7 — Pay Any Tax Owed (or Receive Your Refund)

After filing, one of two things will happen:

If You Owe Tax

Pay your tax by the March 15 deadline using one of these methods:

• Direct bank transfer (振替納税, furikae nozei) — set up automatic payment in advance
• Convenience store payment — pay using the payment slip sent to you
• Credit card — pay via the NTA website (a processing fee applies)
• Pay-easy — available at ATMs and internet banking

If You Are Due a Refund

If your employer over-withheld taxes during the year, you will receive a refund (還付金, kanpukin) deposited to your Japanese bank account:

• e-Tax filers: approximately 3 weeks
• Paper filers: approximately 1–2 months

Make sure your bank account information is correctly entered in your tax return.

For a detailed guide on taxes, social insurance, and pension obligations, see this tax and social insurance guide at For Work in Japan.

Step 8 — Pay Your Resident Tax (Juminzei)

Resident tax (住民税, juminzei) is separate from national income tax and is collected by your prefecture and municipality. It equals approximately 10% of your previous year's income (4% prefectural + 6% municipal).

Important Things to Know

• You are assessed based on your residency status on January 1 of each year
• If you were in Japan on January 1 and had taxable income the previous year, you will owe resident tax regardless of your nationality or visa type
• Bills are sent out around June by your local city/ward office
• Resident tax can be paid in four installments (June, August, October, January) or in full

For Salaried Employees

Most employers deduct resident tax automatically from your salary each month (特別徴収, tokubetsu choshu). You usually don't need to do anything.

For Self-Employed or Those Who Left a Job

You will receive a payment slip and need to pay directly. Use the slip at convenience stores, banks, or through internet banking.

Warning for those leaving Japan: If you leave Japan after January 1, you will receive resident tax bills starting in June. You must either pay before leaving or appoint a tax representative (納税管理人, nozei kanrinin) in Japan to handle payments on your behalf.

Step 9 — Consider Using a Tax Accountant (Zeirishi)

If your tax situation is complex — overseas income, running a business, multiple income streams, or significant investments — hiring a certified tax accountant (税理士, zeirishi) can save time and reduce risk.

When a tax accountant is worth it:

• Annual income over ¥10 million
• Business income with multiple deductible expenses
• Overseas assets or income requiring complex reporting
• Real estate investments
• First year filing as self-employed

Costs vary, but typically range from ¥30,000 to ¥100,000+ per filing depending on complexity. Many zeirishi offices have English-speaking staff or can provide documents in English.

For IT workers and professionals with side income, this tax filing guide for IT workers on Ittenshoku explains when self-filing vs. accountant makes sense.

Special Considerations for Foreigners

Blue vs. White Tax Return (for Self-Employed)

Self-employed foreigners can choose between two filing types:

The blue return (ao-iro shinkoku) requires advance registration with your tax office and maintaining proper double-entry accounting records, but offers a significantly larger tax deduction.

Overseas Income

As a Non-Permanent Resident, foreign income that is NOT remitted to Japan is generally exempt from Japanese tax. However, once you become a Permanent Resident, all worldwide income must be reported — including overseas bank accounts, foreign investment gains, and rental income abroad.

Leaving Japan Mid-Year

If you leave Japan permanently, you must:

1. File a final tax return before departing (or appoint a tax representative)
2. Apply for a lump-sum pension refund (脱退一時金, dattai ichijikin) within 2 years of departure
3. Ensure all resident tax obligations are settled

For comprehensive information on working life and financial obligations in Japan, check out The Complete Guide to Working in Japan as a Foreigner.

Tax Filing Checklist

Use this checklist before filing your Japanese tax return:

• [ ] Determined your tax residency status (non-resident / non-permanent resident / permanent resident)
• [ ] Received your gensen choshu hyo from your employer
• [ ] Collected all income records (salary, freelance, investments, overseas income)
• [ ] Gathered receipts for deductions (medical expenses, social insurance, Furusato Nozei)
• [ ] Prepared My Number Card and bank account information
• [ ] Chosen filing method (e-Tax, mail, or in-person)
• [ ] Filed before March 15 deadline
• [ ] Paid any remaining tax owed or confirmed refund bank details

Conclusion

Paying taxes in Japan as a foreigner involves several layers — national income tax, resident tax, and potentially social insurance — but the process is manageable once you understand it. For most salaried employees, your employer handles the heavy lifting through year-end adjustment. If you are self-employed, have side income, or overseas earnings, filing a kakutei shinkoku is a once-a-year task that becomes easier with each filing.

Use e-Tax for convenience, file early to avoid the rush, and when in doubt, consult a bilingual tax accountant.

For more on managing your finances as a foreigner in Japan, explore The Complete Guide to Banking and Finance in Japan and The Complete Guide to Cost of Living in Japan.

Additional resources:

• Japanese Income Tax Guide for Foreign Workers 2025 – Japan Handbook
• How to File Your Tax Return in Japan – MailMate
• Japan Income Tax Guide – Expatica