Cheat mode
At the title screen, hold Z and press A, B, R, A(2), B, R, A to unlock all selections in the Puzzle University.

Very Hard Mode
To open "V-Hard" (very hard) mode in Pokémon Puzzle League select the game as normal, and in the first Game Settings screen do the following:
Hold Z then tap L, L, A and then B.
Note: To earn this code Beat the game on hard mode

High speed marathon mode
At the title screen, hold Z and press B, A, L(2) to be able set the starting speed in marathon mode to a maximum of 99. Alternately, score at least ten thousand points in the time zone.

Bonus trainers
At the trainer selection screen, hold L + R + Z on controller one and two to unlock the trainers marked by a "?". Alternately, successfully complete the Spa Service.

Mewtwo's stage
At the trainer selection screen, hold Z and press B, Up, L, B, A, Start, A, Up, R to start the game in Mewtwo's stage. Player one will be Ash, player two will be Mewtwo. Alternately, successfully complete the game on the "S-Hard" difficulty setting.