At any decent size train stations in Japan you should have no problem finding bento (or it is called Ekiben, 駅弁, if it sold at train stations ) in the morning to take with you. Especially in large cities there should be no problem. More you go to country side of Japan you will find less stores open during morning commute time.

Should add, convenience stores such as 7 Eleven in Japan sell bento. If you are at a not so major train station and see a convenience store right near the station then you can buy one to go at a convenience store.