This version is a celebratory release from Taito for having 3000 active Densha de Go! 2 arcade units nation-wide in Japan, titled Densha de Go! 2 Kousoku-hen 3000-bandai. It adds eleven new routes and several new train models. Upgrade kits and new cabinets were made available in August/September 1998.

This version was ported to Dreamcast and Windows PC in 2000. It also serves as the basis for 1999's Densha de Go! 64.