The player directs Professor Hector to jump onto buttons, each of which activates an action for the Robotic Operating Buddy (R.O.B.) accessory. A given sequence must be followed in order for R.O.B. to arrange the colored discs in the correct order on the 5 pedestals surrounding it. Stack-Up is considered to be a rare game, especially outside of the USA, with the discs being among the hardest to find accessories for the NES.
Like the other R.O.B game Gyromite, the game uses a series of screen flashes to tell R.O.B. what you want him to do.