The SEGA Saturn was the first console version of Children of the Atom to be released, and was also Capcom's first SEGA Saturn game. It's a good port, whilst some animation has been cut, the Saturn version plays well and has all of the characters, moves and stages, along with some extras. It would remain the best console version of the game for a very long time.

This version has more modes of play. The survival mode has you fight each character in the game, with matches consisting of just one round. The catch is that you only regain a small amount of health between each round. Group battle mode is for two players only, and lets you pick teams of characters, King of Fighters style, and then take on the opponent's team. When you defeat your opponent's first character, the next battle will be against their second character and so on.

A cheat code lets you play as Juggernaut, but only in the versus mode. This means the PlayStation version has an advantage of the Saturn version in terms of playable characters, at it has a cheat code that lets you use both Juggernaut and Magneto in versus mode. But in all other aspects the Saturn version is superior. It wouldn't be until 2024, when Marvel Vs. Capcom Fighting Collection Arcade Classics was released, that this version would be rendered osolete.