As a cinematic platformer, Flashback features gameplay similar to that of 1989's Prince of Persia, and Delphine's own Another World released in 1991. Each level spans a large number of non-scrolling screens, nearly all of which feature multiple levels of altitude — requiring the player character Conrad to jump, grab onto ledges, climb, use elevators, and drop onto lower levels. Conrad exhibits realistic human running speed and jumping ability, as well as realistic weakness — he will die if he falls from too great a height.

Conrad also carries a pistol with unlimited ammunition, a force shield which absorbs a certain number of shots before needing recharging, acting as Conrad's health, how many attacks he can survive before dying, and a portable force field with unlimited use, which can act as a temporary barrier to block enemies' shots.

As Conrad progresses through the game's seven levels, he is increasingly presented with spatial puzzles, requiring the player to discover how to guide him toward his destination. Late in the game, Conrad receives a teleportation device, and is able to progress by throwing the device and teleporting into otherwise unreachable areas.