Yes, Japan doesn't really have anything like the Night Markets of Chinese and Taiwanese cities. In some of the more traditional residential areas near train stations, you may find street vendors, especially vendors of yakitori, noodles, and oden, who come out at night to feed the salarymen and others who have been working or drinking late, but rarely more than one or two on any given street.
Your other option for street food is festivals. Look up the festival listings under the Entertainment tab on the Japan Times website, which include directions for how to get to the festival site by public transit and some idea of what the festival is about. You'll usually find a dozen or so food booths and carts at the larger festivals.
However, most residential neighborhoods that are near train stations are full of small, mom-and-pop restaurants. They have all the local atmosphere that you could want.