Summary
If you make 39,709,284 円 a year living in Japan, you will be taxed 14,340,757 円. That means that your net pay will be 25,368,527 円 per year, or 2,114,044 円 per month. Your average tax rate is 36.1% 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 41.01 円, hence, your net pay will only increase by 58.99 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 2,950 円 of net incomes.