The Master System version of Where in the World Is Carmen Sandiego keeps the gameplay mechanics of the computer original. The main difference is the interface: instead of navigating text menus, the player directly controls the detective through the side-scrolling cities. There are two landmarks to look out for: buildings (entering them allows to question people) and a phone booth to enter the suspect's characteristics (eye color is replaced with vehicle). If the player is on the correct track, the suspect may show up and take a shot - the player must jump over it in order to avoid losing time.
The gameplay involves tracking down Carmen Sandiego and her accomplices, known as V.I.L.E. (Villains' International League of Evil), across various countries. The player must navigate through levels, questioning people, gathering information, and avoiding obstacles. With a variety of suspects to investigate, the game requires strategic thinking and quick reflexes.