Summary
If you make 41,904,000 円 a year living in Japan, you will be taxed 15,271,720 円. That means that your net pay will be 26,632,280 円 per year, or 2,219,357 円 per month. Your average tax rate is 36.4% and your marginal tax rate is 45.9%. 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 45.86 円, hence, your net pay will only increase by 54.14 円.
Bonus Example
A 1,000 円 bonus will generate an extra 541 円 of net incomes. A 5,000 円 bonus will generate an extra 2,707 円 of net incomes.