Ganbare Goemon! Karakuri Dōchū plays as a top view action/adventure game though it is separated by stages. In each level Goemon must find three passes in order to advance. Some of these passes are found in boxes, secret passages or can be bought. After finishing all the stages, the game will present the player with a new Japanese province, but all the levels will remain the same. The ending, however, will be different.
Like the rest of the series, Goemon can be powered-up if certain items are found and/or bought, which can be lost after a few hits.