The player makes his way along a Yamato-e painting landscape fighting enemies as they appear. The game offers three types of action: Small Mode (standard), Big Mode (standard, but with large characters and usually boss fights) and Plain Mode (viewed from an overhead perspective). Most stages have torii, which are used to transport the player to a different stage. On most stages featured in Side Mode and Plain Mode, there are multiple torii that can be entered which will lead to different routes on the map. In Big Mode, however, there is only one torii at the end of this type of stage.
The leading character is a historical Japanese samurai, Taira no Kagekiyo (also known as Akushichibyōe Kagekiyo) who fell in the Battle of Dan-no-ura at the end of the Genpei War. In Genpei Tōma Den, he was resurrected and fights Minamoto no Yoshitsune and Saito Musashibo Benkei over the Imperial Regalia of Japan, as well as to defeat his enemy Minamoto no Yoritomo.
The game also features the Sanzu River, a place believed in Japanese Buddhism to separate "the current life" and "the afterlife", resembling the concept of the Underworld or Hell (The river is often compared to the river Styx in Greek mythology). Therefore, some mythological characters like Emma-o (literally "Enma Dai-o"), god of the Underworld, and the Sun Goddess Amaterasu appear in the game.