Nintendo made black cartridges that were compatible with the Game Boy Colour, the older Super Game Boy and the original Game Boy. The black colour distinguished these special cartridges from the grey Game Boy carts and the transparent Game Boy Colour carts. The black cartridges had notches in the corner like old Game Boy cartridges, allowing an original Game Boy to be turned on when they were inserted, while the Game Boy Colour cartridges did not. Special Game Boy Colour palettes were built into the black carts, making it impossible to change their palette. Game Boy Colour games also feature the different colour cartridges for the European and American releases of the Pokémon games.

The processor, which is a Z80 clone made by Sharp with a few extra (bit manipulation) instructions, has a clock speed of approx. 8 MHz, twice as fast as that of the original Game Boy. The Game Boy Colour also has four times as much memory as the original (32 kilobytes system RAM, 16 kilobytes video RAM). Additionally, the Game Boy Colour could address more ROM, allowing games as much as eight times the maximum size of those for the original Game Boy. The screen resolution was the same as the original Game Boy, which is 160x144 pixels.

The Game Boy Colour also featured an infrared communications port for wireless linking. However, the feature was only supported in a few games, and the infrared port was dropped for the Game Boy Advance and later releases. The console was capable of showing up to 56 different colours simultaneously on screen from its palette of 32,768, and could add basic four-color shading to games that had been developed for the original Game Boy. It could also give the sprites and backgrounds separate colours, for a total of more than four colours. This, however, resulted in graphic artefacts in certain games; a sprite that was supposed to meld into the background was now coloured separately, exposing the trick.