You might be thinking, “I really should file my taxes online this year,” but you may also be feeling anxious because e-Tax seems too complicated to use.
e-Tax is the government’s online service for filing and paying national taxes like income tax and consumption tax. It’s convenient because you can complete your tax filing procedures online without having to visit the tax office or mail in paperwork.
Plus, if you use accounting software that works with e-Tax, you can sync your data directly. This means less paperwork and more efficient day-to-day administrative tasks.
In this article, we’ll walk you through everything from who needs to file taxes to how to submit your tax return using e-Tax, so even first-timers can get through it smoothly. We hope you find it helpful.
Village House offers over 1,000 affordable properties across Japan with rent starting from ¥ 20,000 per month. If you’re thinking about moving, check out our website.
Check whether you need to file a tax return (確定申告)
Whether you need to file a tax return depends on your annual income and specific circumstances. Many people also qualify for tax refunds when they file their taxes.
For example, if you have deductions for medical expenses or hometown tax donations, filing a return can get you back taxes you overpaid. It’s helpful to think of tax filing not just as an obligation, but as something you can use to your financial advantage when appropriate.
If any of the following apply to you, you’ll need to file a tax return:
Individuals who are self-employed or freelance and exceed the basic deduction (基礎控除)
If you’re self-employed or freelance with income, check whether your total income (合計所得金額) exceeds the basic deduction amount.
According to the basic deduction table for tax year 2025 (Reiwa 7) and onward, if your total income is 1.32 million yen or less, the basic deduction amount is 950,000 yen. Therefore, once your income goes over 950,000 yen, you’ll need to file a tax return.
| Taxpayer’s Total Income Amount (合計所得金額) | Deduction Amount (控除額) | ||
| Before Tax Year 2024 | Tax Year 2025 / Tax Year 2026 | Tax Year 2027 and After | |
| ¥ 1.32 million or less | ¥ 480,000 | ¥ 950,000 | ¥ 950,000 |
| ¥ 1.32 million to 3.36 million or less | ¥ 880,000 | ¥ 580,000 | |
| ¥ 3.36 million to 4.89 million or less | ¥ 680,000 | ||
| ¥ 4.89 million to 6.55 million or less | ¥ 630,000 | ||
| ¥ 6.55 million to 23.5 million or less | ¥ 580,000 | ||
| ¥ 23.5 million to 24 million or less | ¥ 480,000 | ¥ 480,000 | |
Source: National Tax Agency | Basic Deduction
Note that the Reiwa 7 regulations take effect on December 1, 2025, so check the Tax Reform Q&A for Fiscal Year 2025 (Reiwa 7) (Related to Basic Deduction Revisions, etc.) (May 2025) for details on what applies before that date.
People with a side income of over ¥ 200,000
If you’re a salaried employee who receives year-end adjustment (年末調整), and you have additional income (side jobs, part-time work, online auction sales, etc.) exceeding ¥ 200,000 annually, you need to file a tax return. Keep in mind that “income” means revenue minus necessary expenses, so if your income after expenses is ¥ 200,000 or less, you generally don’t need to file one.
Sources:
National Tax Agency | When Salaried Employees Earn Side Income from Online Auctions, etc.
National Tax Agency | Wage Earners Who Must File a Final Tax Return
People who haven’t had their year-end tax adjustment (年末調整) done due to changing jobs
If you’re a company employee, you generally don’t need to file a tax return. However, you will need to file one if any of the following apply:
- You did not start a new job within the same year
- You did not submit your withholding slip (源泉徴収票) from your previous employer to your new employer
- Changed from self-employment or freelance to company employment
People with a salary income of over ¥ 20 million
Year-end adjustment typically applies to salaried employees earning ¥ 20 million or less. If your salary exceeds ¥ 20 million annually, your employer can’t settle your taxes, so you need to file them yourself.
Source: National Tax Agency | Tax Filing for Salaried Employees
Documents and information to prepare before filing
- My Number card or ID/Password
To file your tax return through e-Tax, you need either a My Number Card or an ID/password obtained beforehand from the tax office or online.
- My Number card PIN
If you are using your My Number Card, you’ll need to enter the PINs you set when the card was issued (user authentication PIN and signature PIN). Make sure you remember them, as you can’t proceed without them.
- Withholding slip (源泉徴収票)
Salaried employees filing online need their withholding slip to enter information about social insurance premiums deducted from their salary and income tax amounts.
- Deduction-Related Documents
| Income Deduction (所得控除) | Required Documents |
| Social Insurance Premium Deduction (社会保険料控除) | Social Insurance Premium (National Pension Insurance) Deduction Certificate |
| Small Enterprise Mutual Aid Premium Deduction (小規模企業共済等掛金控除) | Proof of premium payments |
| Life Insurance Premium Deduction (生命保険料控除) | Proof of premium payments |
| Earthquake Insurance Premium Deduction (地震保険料控除) | Proof of premium payments |
| Working Student Deduction (勤労学生控除) | Certificate issued by the school |
| Disability Deduction (障害者控除) Spouse (Special) Deduction (配偶者控除・配偶者特別控除) Dependent Deduction (扶養控除) | For non-resident relatives claimed as dependents: ・Family relationship documents ・Remittance-related documents |
| Casualty Loss Deduction (雑損控除) | Receipts for unavoidable disaster-related expenses |
| Medical Expense Deduction (医療費控除) | Medical expense deduction certificate |
| Donation Deduction (Hometown Tax) (寄附金控除・ふるさと納税) | Donation receipt issued by the organization or entity you donated to |
Source:
National Tax Agency | Tax Filing Guide, Documents to Attach/Present
National Tax Agency | Hometown Tax (Donation Deduction)
- Bank account (for Receiving Refunds)
If you overpaid taxes, the refund gets deposited into your bank account. Have your bank name, branch name, and account number ready.
It’s a good idea to keep all your tax filing documents, withholding slips, insurance premium deduction certificates, medical expense receipts, and My Number-related documents together in one file to avoid losing anything or leaving something out.
Setting up e-Tax for the first time
Filing using a smartphone
- Check if your phone can read My Number Cards
- Prepare your My Number Card’s user authentication and signature certificate PINs
- Log in to the tax document creation corner (確定申告書等作成コーナー) and complete the initial setup
Source: National Tax Agency | e-Tax with Smartphone and My Number Card
Filing using a computer
- Verify your computer meets the recommended requirements
- Download any necessary setup tools or extensions
- Get an IC card reader to scan your My Number Card
- If using your smartphone to read your My Number Card, scan the QR code to link it with the My Number Portal app
- Log in to the tax document creation corner (確定申告書等作成コーナー) and complete the initial setup
Source:
National Tax Agency | Using e-Tax Software (Web Version) [Computer]
National Tax Agency | e-Tax QR Code Authentication
Logging in to e-Tax using your My Number card
How to log in to the tax document creation corner using your My Number Card
- Go to the tax document creation corner and select “My Number Card Method” to log in
- Read your My Number Card using an IC card reader or smartphone
- Enter your My Number Card’s user authentication certificate password, and you’re logged in
If your card can’t be read
- For iPhone, hold the center of your My Number Card against the top of your phone and keep it still for several seconds
- For Android, hold the center of the card against the “contactless IC mark” on the back of your device and keep it still
- Remove card cases and phone covers
- Disconnect charging cables and earphones
- For Android, check that the NFC (Mobile Wallet) function is turned ON
Be careful if you enter the wrong user authentication certificate password (4-digit number) three times in a row, it locks. If it gets locked or you forget it, you can reset or reinitialize the password at a convenience store kiosk terminal.
Source:
National Tax Agency | e-Tax with Smartphone and My Number Card!
Digital Agency | Reading IC Chips with Smartphones
Entering your income information
Transfer the numbers from your withholding slip (源泉徴収票): payment amount (支払金額), withholding tax amount (源泉徴収税額), social insurance premium amount (社会保険料等の金額), and total deduction amount (所得控除の額の合計). If your company provided an XML data file, you can automatically retrieve it through the My Number Portal linkage.
Your withholding slip must show that the year-end adjustment (年末調整) is complete. If the payment amount is ¥ 20 million or less and there’s an amount filled in either the “amount after employment income deduction (給与所得控除後の金額)” or “total deduction amount (所得控除の額の合計)” field, the year-end adjustment is complete.
If you’re self-employed, freelance (business income 事業所得), or have side income (miscellaneous income 雑所得), enter it in the respective input screen. Typically, you’ll enter sales (売上) and expenses (経費) separately.
To avoid input errors, double-check these items:
- Does the withholding slip amount match what you entered?
- Did you mix up similar-looking numbers like “0 and 6” or “7 and 1”?
- Did you accidentally swap income and expenses for side jobs/freelance work?
Source: National Tax Agency | Tax Document Creation Corner Input Manual
Claiming deductions you’re likely eligible for
Common Deductions
| National Pension Insurance Premium Deduction (国民年金保険料控除) | If you pay your national pension insurance premiums yourself, you can claim them as a social insurance premium deduction (社会保険料控除). |
| National Health Insurance Premium Deduction (国民健康保険料控除) | Just like national pension premiums, if you pay your national health insurance premiums yourself, you can claim them as a social insurance premium deduction. |
| Life Insurance Premium Deduction (生命保険料控除) | If you pay premiums for life insurance, nursing care/medical insurance, individual pension insurance, etc., you can claim a life insurance premium deduction based on the amount paid. |
| Medical Expense Deduction (医療費控除) | Medical expense deductions generally apply to medical costs exceeding ¥ 100,000 per year (or 5% of your total income if your total income is less than ¥ 2 million). Source: National Tax Agency | When You Pay Medical Expenses (Medical Expense Deduction) |
| If You Have Changes in “Commuting Distance” Due to Moving | If you need to relocate due to a job transfer or reassignment at work, those moving expenses and commuting costs may qualify as “specific expense deductions (特定支出控除).” However, depending on your circumstances, you might not qualify for the deduction, so check the National Tax Agency’s guidelines on specific expense deductions for salaried employees. |
Steps for entering deductions
- Open the income/deduction input screen in the tax document creation corner
- Enter national pension and health insurance payment amounts under social insurance deduction (社会保険料控除)
- Enter insurance payment amounts under life insurance deduction (生命保険料控除)
- Select the medical expense deduction (医療費控除) or the self-medication tax system (セルフメディケーション税制), and enter total amounts from receipts and statements
- After entering all applicable deductions, run the automatic calculation (自動計算)
- Confirm that deduction amounts, income amounts, and tax amounts are correct on the confirmation screen
Tips for increasing your refund
The more deductions you enter, the lower your taxable income. This means you’re more likely to get back taxes that were over-withheld.
Reviewing and submitting your return
- Review your entries
Once you’ve finished creating your tax return, double-check that income amounts (収入金額) and deduction items (控除項目) are correct.
- Confirm your refund amount
If your deductions are entered correctly, your taxable income decreases and your refund increases. Check the “estimated refund amount (還付金の見込み額)” displayed on the return screen and make sure it’s roughly what you expected.
- Verify you name and bank account information
Before submitting electronically, make sure your name, address, and bank account are correct. Mistakes can delay your refund or trigger inquiries from the tax office.
- Submit your tax return
Once everything’s ready, submit your electronic return. Once the submission is complete, the dialog window will close and the “Immediate Notification Result” screen will appear.
Source: e-Tax | Data Transmission (Sending and Confirmation)
After you file: Refund timeline and what to save
When refunds are deposited (around 2 weeks)
If you file electronically through e-Tax and there are no issues, your refund is typically processed in about two weeks.
Source: e-Tax | Checking Refund Processing Status
What to do if you get a notice from the tax office
If you applied for your tax refund using the My Number method, you can check the status once the refund has been processed. You’ll receive either a postcard titled “National Tax Refund Deposit Notification (国税還付金振込通知書)”, or a notification in your e-Tax message list. If you opted for electronic notification, you won’t get a postcard.
When you receive the notification, verify the details (deposit date, amount, bank account, etc.). If there are any discrepancies or errors, contact your local tax office as needed.
Source: e-Tax | Electronic Notification for Refund Transfers
Documents to Save for Next Year
| Withholding Slip (源泉徴収票) | Proof of salary income, etc. |
| Payment Certificates/Deduction Certificates | Proof of life insurance premium deductions, social insurance premium deductions, medical expense deductions, etc. |
| Electronic Filing Records and Other Tax Return Documents | For self-employed individuals, the required retention period varies by document type, but tax return-related documents must generally be kept for 5 to 7 years. |
Source: National Tax Agency | Bookkeeping and Document Retention/Blue Return
Summary
Here’s what we covered about who needs to file a tax return and how to do it online using e-Tax:
- Whether you need to file a tax return depends on your annual income and circumstances
- Filing your taxes can potentially get you a tax refund
- Using e-Tax means you don’t have to go to the tax office or mail paperwork
- Linking with compatible accounting software makes administrative work more efficient
- To file your taxes return through e-Tax, you need your My Number Card and PIN, or an issued ID/password
- Keep withholding slips (源泉徴収票) and deduction documents organized together in one file
- You can file your tax return through e-Tax using either a smartphone or a computer
- If there are no issues, refunds are typically deposited within about two weeks
Properties offered by Village House come with no key money, security deposits, guarantor fees, or renewal fees (※). If you want to save on initial moving costs, feel free to contact us.
※Please note that, depending on contract terms and screening results, a security deposit may be required in some cases.
Related articles:
Hello, I’m Machiko Doi, a freelance writer who writes about housing and living in Japan.
I live in an 80-year-old house that I inherited from my grandparents along with my two shelter cats and daughter.
We live a relaxed life while repairing the house.
I like to cook vegetables from the garden and fresh fish caught by my father, and enjoy them with cold beer on a hot day or hot sake on a cold day.