"Pokémon Puzzle League" features the same gameplay as in "Panel de Pon". The objective is to clear blocks from the playfield by arranging them in horizontal or vertical lines of three or more blocks. A continuous stream of new blocks pushes up from the bottom of the playfield, causing the entire playfield to rise continuously. If the blocks reach the top of the playfield, the player loses. The player can temporarily stop the progression of blocks by scoring combos and chains, and in two-player battles, these actions also cause garbage blocks to stack on top of the opponent's playfield.