Puzzle University

In Pokémon Puzzle League, there are 260 predefined puzzles, distributed this way:

• the class I with 30 basic puzzles
• the class II with 30 basic puzzles, 10 action puzzles, and 10 3D puzzles
• the class III with 30 basic puzzles, 10 3D puzzles, and 10 action puzzles
• the class special I with 30 basic puzzles
• the class special II with 40 basic puzzles and 10 action puzzles
• the class special III 30 basic puzzles, 10 3D puzzles, and 10 3D puzzles

Additionally, there are 15 available slots for custom puzzles.

The Puzzle University is found at the northwestern corner of the Puzzle Village map, which serves as the main menu at the start of the game.

There are 7 save slots with the names of each player, plus an additional "Guest" slot where no data is saved. An unused save slot is displayed as "(New)". These slots are used not only in the Puzzle University, but in other modes as well (such as Stadium, Marathon, and Spa Service). The player may choose any slot and press A to play, or press Z+A to completely delete that save slot. If the player chooses a slot with saved Puzzle data, there are "Continue" and "New game" options.

The progress screen contains a list of solved and unsolved puzzles. When a round is available, the player is able to choose any puzzle from that round.

Unlike in Pokémon Puzzle Challenge, there is no countdown before each puzzle starts, so the player is able start playing immediately. The player is required to clear all the blocks from the playing field. However, they are only allowed to move the blocks a certain number of times, which is displayed at the right side of the screen. The recurring Jigglypuff from the anime tells the number of remaining moves. The player may press B at any time to return the blocks to the previous state, except they don't have the chance to do this after the last move has been used, which ends the current puzzle immediately.

When the player successfully solves a puzzle, there is a fireworks animation, and the next puzzle appears automatically.

Unlike in Pokémon Puzzle Challenge, there are no available hints in this game.

The timer displays the total amount of time the player has taken in all puzzles from that save slot, regardless of whether the player has solved or failed the previous puzzles. However, if the player shuts down the game system during an ongoing puzzle, the time taken in the current puzzle will not be added to the timer.

The player may press Start to pause either game, which opens a menu with the options below.

Whenever the player solves a puzzle, the current progress is automatically saved.