Summary
If you make 53,542,372 円 a year living in Japan, you will be taxed 20,619,550 円. That means that your net pay will be 32,922,822 円 per year, or 2,743,569 円 per month. Your average tax rate is 38.5% and your marginal tax rate is 46.1%. 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 46.11 円, hence, your net pay will only increase by 53.89 円.
Bonus Example
A 1,000 円 bonus will generate an extra 539 円 of net incomes. A 5,000 円 bonus will generate an extra 2,695 円 of net incomes.