Mario Bros. Special is based on, but very different from, the original arcade game. Much like the original title, the action takes place on single screens, but the objective on each stage is no longer simply to kill all the enemies. There are four different screens, which cycle in order with increasing difficulty.

The first screen sees Mario attempting to reach the top of the screen through moving gaps, at the top of the screen are five switches, and if all five are active simultaneously, the exit gate will open. The second screen features trampolines, which Mario can use to stun enemies, kill all the enemies and an exit platform will appear. The third screen includes conveyor belts which can be used much like the trampolines to stun enemies, the goal here however is to collect money, and eventually a ring will appear at the top of the stage which must be collected. The fourth and final screen is a bonus screen filled with money, collect all the money before the time limit, and another ring will appear, giving bonus points.