After setting the time and choosing a name, Professor Birch tells the player that he found rare eggs. However, he is too busy to take care of them, so he gives the player a choice between a Torchic, a Treecko, or a Mudkip to hatch and raise. The player's first task is to place the egg into a basket and stroke it until it hatches. The player interacts with the Pokémon using the D-pad to move a cursor around the interface. The player can pet, play with, and drag their Pokémon with this cursor. They can also interact with background objects such as a light switch and a drawer. Unlike standard virtual pet video games, the player's goal in Pokémon Breeder mini is not to keep the Pokémon alive but rather to train it in three out of four different skill categories. The game allows the player to train their Pokémon by playing with it using various toys, feeding it Pokéblocks, and playing with it outside in various challenges.

After setting the time and choosing a name, Professor Birch tells the player that he found rare eggs. However, he is too busy to take care of them, so he gives the player a choice between a Torchic, a Treecko, or a Mudkip to hatch and raise. The player's first task is to place the egg into a basket and stroke it until it hatches. The player interacts with the Pokémon using the D-pad to move a cursor around the interface. The player can pet, play with, and drag their Pokémon with this cursor. They can also interact with background objects such as a light switch and a drawer. Unlike standard virtual pet video games, the player's goal in Pokémon Breeder mini is not to keep the Pokémon alive but rather to train it in three out of four different skill categories. The game allows the player to train their Pokémon by playing with it using various toys, feeding it Pokéblocks, and playing with it outside in various challenges.