Summary
If you make 2,409,960 円 a year living in Japan, you will be taxed 458,956 円. That means that your net pay will be 1,951,004 円 per year, or 162,584 円 per month. Your average tax rate is 19.0% and your marginal tax rate is 20.9%. 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 20.86 円, hence, your net pay will only increase by 79.14 円.
Bonus Example
A 1,000 円 bonus will generate an extra 791 円 of net incomes. A 5,000 円 bonus will generate an extra 3,957 円 of net incomes.