Box Boy! is a platform game in which players control a box-shaped character named Qbby as he makes his way through each level. The source of the game's mechanics come from Qbby's ability to spawn boxes out of his body, the number of which varies between each level. These boxes can spread out in whatever direction is possible to make various shapes and can either be carried or thrown and pushed around. The boxes have various uses, such as allowing players to reach high ledges or cross large gaps, holding down switches, or blocking deadly lasers. Additionally, by hooking these boxes onto a ledge while Qbby is still attached, he can pull himself up.

Each level features one or more crowns, which can be collected with advanced play but will become uncollectable if the player uses too many boxes during a level. These crowns unlock additional worlds as the game progresses. Medals obtained from clearing each level can be spent on extras, such as costumes, technique manuals, and bonus levels.