Players can control Godzilla through a transmitter on the Super X2 as he attempts to thwart the alien invaders that have come to destroy humanity in their UFOs. The aliens have also the ability to control some of Godzilla's greatest adversaries. During the game, Godzilla is revealed to have the power to transform into Super Godzilla after finding three capsules of Super S energy.
Godzilla will begin at a certain location on battle zone that is displayed on the map view in the lower half of the player's screen. Each zone is split up in up to 8 map sections. Godzilla will automatically move in whichever direction he is facing and change zones until the player orders him to move in another direction. Godzilla's movement speed is affected by whatever terrain he happens to be traveling through, such as moving significantly slower if he is in deep water. As Godzilla moves through the level, he may tread across traps, smash buildings, or encounter enemies, all of which will lower his health. Each zone also contains a variety of power-ups and restoration stations for Godzilla to find. Godzilla can hold up to four colored orbs at a time to use in combat. The player must find and destroy the Mother UFOs and the enemy monsters in each level within a given time limit, or the game will end.
Combat switches from the split-screen map perspective to one where the top plays like a fighting game while the bottom shows special abilities the player may be able to activate. Godzilla's special abilities include his powerful breath attacks, a tail whack, a body slam, a bite attack, and the ability to use items.
King Ghidorah - The first level boss. King Ghidorah is causing havoc in Osaka, and destroys Osaka Castle.
Mechagodzilla - After encountering the Mother UFO on Mt. Fuji, Godzilla finds another Godzilla in the second level. The fake Godzilla is quickly revealed to beMechagodzilla, who has the ability to use a shield to reflect Godzilla's breath attacks. In the Japanese version of the game, there is no fake Godzilla and instead of fighting the original version of Mechagodzilla, players encounter the 1993 version.
Biollante - Created from the cells of Godzilla, Biollante is a massive sea monster hiding out in Lake Ashino. She attacks with two massive tentacles, is immune to Godzilla's body slam, can hide underwater, and can perform devastating acid attacks.
Battra - Encountered in Yokohama, Battra is one of the easier enemies in the game. He has low defense, and can easily be dispatched with one of Godzilla's ultra breath attacks.
Mecha King Ghidorah - Ghidorah has been brought back to life by the alien invaders, and they've given him a new fearsome mechanized head.
Bagan - The only new monster to the Godzilla franchise in the game. Bagan was intended to fight Godzilla in a movie based off the game, but that never came to be. He has powers such as the ability to fire massive plasma beams from his mouth, and send a storm of diamonds at his opponent, and a final transformation.
- The Japanese version of the game's design for Super Godzilla was later used as the direct influence for Space Godzilla. Space Godzilla features only minor cosmetic changes from the Super Godzilla design.
- Bagan is the most famous of the unused monsters of Toho. He only makes his debut on Super Godzilla on the SNES and no where else. It seems Bagan has a problem wherein everytime Toho studios starts to make a film about him, they always decide to scrap it at the last minute.
- Mothra was also planned to be a playable character in the game. He would have been unlocked after defeating Battra.