In Godzilla: Kaijuu Daikessen, players select from one of eight different monsters from the Godzilla movies and battle in a variety of locations. The game was released in Japan only. According to Nintendo Power, the game was planned to be released in North America in April 1995 under the title Godzilla: Destroy All Monsters. However, it was never released.

In the single-player game, players are able to choose from Godzilla himself, Anguirus, King Ghidorah, Gigan, Megalon, Mechagodzilla, Biollante and Mothra. No matter which monster the players select, they are taken to a map of Japan and must select their opponent to battle. Battles take place in the familiar 2D fighting screen seen in Street Fighter II and other games of the genre, though the game plays more akin to the SNES Dragon Ball Z: Super Butōden fighting games. Each round has a time period of sixty seconds, during which each monster fights with a variety of attacks to wear their opponent's energy bar down and win the round. At the end of the round, the player's score is tallied up based on time, energy and the level of their opponent. Once every enemy monster has been defeated, the player enters the eighth and final round and must face Mechagodzilla/Super Mechagodzilla or Gotengo. Upon the defeat of one of those monsters, the credits roll and the game ends.

Each monster has a variety of standard and unique, special attacks, as well as the ability to block. Standard attacks include light and heavy physical attacks (punch, kick, etc.) and varying degrees of energy-based attacks, a dash attack and a grab attack. Each monster also has the ability to stun the opponent with a loud roar. As a succession of hits is landed, the monster will glow red and be stunned for several seconds, while a separate energy bar fluctuates, either to increase the strength of the monster's attack or the possibility of stunning the opponent. Monsters are able to use their projectile attacks to block oncoming projectiles, similar to Street Fighter II, and sometimes the two can clash in a brief test-of-strength encounter.

The game supports the standard two-player Vs Mode, the only difference being in the player's ability to select Mechagodzilla 2 and Atragon, presumably, to choose their own battleground.