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Nine Pokémon themed minigames can be played in Pokémon Stadium, either as stand-alone games or as part of a tournament. One to four human players may participate, with the rest controlled by the computer. Many of the games utilize button mashing.
- Magikarp's Splash: Four Magikarp have flopped onto land and compete against each other to flop the highest and hit the counter on top of the screen. The Magikarp with the highest count at the end of the time limit wins.
- Clefairy Says: This is a combination of Simon Says and a memory game. Four Clefairy are in class and the teacher shows directions on the board. The player must remember the arrow pattern carefully, then repeat it in a limited time. The Clefairy will then dance the moves; if they make an error, the teacher will bop them with a mallet. The last Clefairy to stay in the game without getting bopped five times is the winner; alternatively, the Clefairy with the least bops at the end of the game is the winner. This is also the hardest of the mini-games.
- Run, Rattata, Run: Four Rattata race on parallel treadmills, and must jump over fences along the track. Whichever Rattata gets first place wins.
- Snore War: This game that requires timing skills. As one of four Drowzee, the players must use Drowzee's Hypnosis attack when the pendulum in the middle of the screen hits the center, or it will start to fall asleep. As the game goes on, the pendulum swings faster. The Drowzee that remains awake the longest wins.
- Thundering Dynamo: Players are randomly either a Pikachu or a Voltorb, charging up a machine with electrical energy. Players must press the button on the N64 controller corresponding to the colored light on the machine. The first Pokémon to fill up the bar underneath it wins the game.
- Sushi-Go-Round: As Lickitung, players move around and lick up the different kinds of sushi available, which are worth different amounts of money. Eating the same type of sushi multiple times in a row gives a bonus resulting in a larger bill. After time runs out, the Lickitung with the most expensive bill wins.
- Ekans' Hoop Hurl: The game combines a ring toss with Whack-A-Mole. It is the only mini-game in which it matters which of the four positions the player is in. Players are one of four Ekans lined up along the bottom of the screen. Diglett will pop up randomly out of the nine holes on the field. Aim and shoot your Ekans (which curls into a hoop) over a Diglett for a point. Sometimes a colored or golden Diglett worth more points will pop up. Whoever scores the most points in the time limit wins.
- Rock Harden: Rocks are thrown at Metapod and Kakuna. Using the ability Harden reduces HP, but not as much as getting hit by a boulder. The last Pokémon standing wins.
- Dig! Dig! Dig!: A group of Sandshrew are digging to find water. Whichever digs to the bottom first wins.