Summary
If you make 9,036,564 円 a year living in Japan, you will be taxed 2,379,739 円. That means that your net pay will be 6,656,825 円 per year, or 554,735 円 per month. Your average tax rate is 26.3% and your marginal tax rate is 27.5%. 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 27.48 円, hence, your net pay will only increase by 72.52 円.
Bonus Example
A 1,000 円 bonus will generate an extra 725 円 of net incomes. A 5,000 円 bonus will generate an extra 3,626 円 of net incomes.