Summary
If you make 41,054,000 円 a year living in Japan, you will be taxed 14,892,325 円. That means that your net pay will be 26,161,675 円 per year, or 2,180,140 円 per month. Your average tax rate is 36.3% and your marginal tax rate is 41.0%. 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 41.02 円, hence, your net pay will only increase by 58.98 円.
Bonus Example
A 1,000 円 bonus will generate an extra 590 円 of net incomes. A 5,000 円 bonus will generate an extra 2,949 円 of net incomes.