Virtual Bart consists of several minigames, similar to Bart’s Nightmare. Unlike Bart’s Nightmare, the game does not feature a hub world and each stage is selected randomly using a spinning roulette wheel. The game consists of six different stages. Gameplay for Dino Bart, Baby Bart, and Pig Bart consists of platforming, while Class Picture, Mount Splashmore, and Doomsday Bart consist of different play styles. All stages feature a time limit. If the time runs out, the player loses a life. Additionally, all stages except for Class Picture feature a health bar, which decreases every time Bart gets hit.
Several stages feature corn dogs that restore Bart’s health, as well as extra lives. Once a stage is completed, it cannot be repeated; if the wheel lands on an already-completed stage, it will continue spinning slowly to the nearest remaining stage panel. If the wheel lands on the skull or corn dog panel (which quickly alternates between showing each item), the player will lose or gain a life, respectively. If the player fails a stage, they lose one life and are taken back to the roulette wheel. Failure when the player has no extra lives prematurely ends the game.
Otherwise, the game ends after all stages are cleared. At a science fair, Martin Prince presents a virtual reality device that displays six educational exhibitions. However, Bart causes the device to malfunction and gets trapped in it. Bart must complete the six programs to escape the machine. If Bart successfully completes every stage, he escapes from the device. Homer then enters the malfunctioning device, which explodes shortly thereafter. If the player gets a Game Over, the system “hangs” and the real Bart is trapped inside the device.