How can I make a year-end adjustment?

Year-end adjustment refers to the procedure to match the total amount of income tax withheld in one year of the salary earner who is an employee and the amount of income tax to be paid in one year.
This year-end adjustment is made in the following order, summing up the amount of salary paid to the person in one year: First, calculate the amount of salary after deduction of salary income from the total amount of salary paid in one year. The amount of salary after deduction of salary income is calculated in the "table of amount of salary after deduction of salary income for year-end adjustment".
Next, deduct income deductions such as dependent deductions from the amount of salary after deduction of salary income.
Next, apply the income tax rate to the amount after deducting this income deduction to the tax amount.
Next, when making special deductions such as housing borrowings at the year-end adjustment, the deduction amount will be deducted from this tax amount.
This tax amount is the income tax amount that the person should pay in one year.
Finally, if the total amount of withholding income tax is greater than the amount of income tax to be paid in one year, the difference will be refunded. Conversely, if the total amount of withholding income tax is less than the amount of income tax to be paid in one year, the difference will be collected. Person targeted for year-end adjustment is person who submits "report such as dependent deduction of salary earner". However, those who receive a salary of more than 20 million yen are not subject to year-end adjustment.

NTA website (outside site)