Summary
If you make 125,199,360 円 a year living in Japan, you will be taxed 53,658,556 円. That means that your net pay will be 71,540,804 円 per year, or 5,961,734 円 per month. Your average tax rate is 42.9% 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.