The 2021 Japan National Championships were held in two stages: the main stage on 9 May 2021, and the final stage on 18 July 2021 (after being postponed from its initial scheduled date of 13 June 2021 due to covid restrictions).

The main stage consisted in an online challenge-type best-of-one tournament with players having to play up at least 10 matches and up to 20. At the end of the tournament, they were order based on final ranking points. The top 50 players received a Day 1 invite to the 2022 World Championships. The following 150 players (see here the list of participants) qualified to compete in the main stage:

• Top 50 players of the 2020 Japan Decisive Battle
• Top 100 players of the 2021 Japan National Championships Qualifier (the same challenge-type tournament used as Pokémon Players IV Qualifier)

The final stage saw the top 20 players from the main stage clash in 5 best-of-one Swiss rounds, at the end of which the 8 best players would play against each other in a best-of-three single-elimination bracket. Players could use a different team than in the main stage. The teamsheets were open for the top 8 players (including Nature information). This event was held live from Tokoname and was streamed online!

The top 8 players received a Day 2 invite to the 2022 World Championships. The top 4 players additionally received a Travel Award for it.

As a final note, an unspecified number of top players from this tournament will be invited to the Pokémon Global Exhibition to be held in October.