Summary
If you make 10,249,344 円 a year living in Japan, you will be taxed 2,732,582 円. That means that your net pay will be 7,516,762 円 per year, or 626,397 円 per month. Your average tax rate is 26.7% and your marginal tax rate is 33.1%. This marginal tax rate means that your immediate additional income will be taxed at this rate. For instance, an increase of 100 円 in your salary will be taxed 33.09 円, hence, your net pay will only increase by 66.91 円.
Bonus Example
A 1,000 円 bonus will generate an extra 669 円 of net incomes. A 5,000 円 bonus will generate an extra 3,346 円 of net incomes.