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Pokémon Battrio's gameplay is simple.

Gameplay is turn-based, and centers around the 4×4 grid shown on the left.

• 1. First, arrange the Pokémon chips on the grid. You can place them in any manner you want, but you can only have three Pokémon on the grid at any one time.
  2. After placing the chips, press the スキャン (scan) button to update the display on the screen.
  3. Push the えらぶ (select) button to display further information about the Pokémon and the arrangements you have placed them in.
     

     An example team arrangement.
  4. If you are not satisfied with the results, rearrange the chips and push the scan button again.
  5. Once you are satisfied with the results, press けってい (confirm).

You will then see short Pokémon Battle Revolution-style animations of the Pokémon using their offensive or or defensive moves. The arrangement and statistics of the Pokémon as well as the arrangement and statistics of the opposing Pokémon will determine how much team health the opponent loses. After this the other player does the same, and then it is the first player's turn again.

The game can last any number of turns; once one of the players' health bars is completely depleted that player has lost the round.