In the competition, the top 13 teams from the 2024–25 Malaysia Super League were joined by the top three teams from the 2024–25 Malaysia A1 Semi-Pro League. The competition was played from 20 November 2024 until TBD 2025, with 16 teams in the knockout stage which began in the round of 16, followed by quarter-finals, semi-finals and the final. This stage was played in two legs, except for the final which was played as a single leg.
For this edition, a total of 16 teams will compete in the tournament, which qualifying results will be determined after week 14 league matches. The top 8 teams from Super League will automatically qualify to the knockout stage as seeded. Super League teams ranked 9th until 13th and A1 Semi-Pro League teams ranked 1st, 2nd and 3rd placed will be drawn as unseeded. Teams that fail to progress to the quarter-finals will automatically continue the challenge at the 2024–25 MFL Challenge Cup.
The seeded teams were drawn against the unseeded teams, with the seeded teams become hosting for the round of 16.
For the draw, the teams were seeded and unseeded into two pots based on the following principles (introduced starting this season). The results seeding will be determined after week 14 league matches:
Pot B contained the 9th until 13th placed teams from 2024–25 Super League, and the 3 teams selected from 2024–25 A1 Semi-Pro League, based on subject approval from the MFL Board of Directors.
In the knockout phase, teams played against each other over two legs on a home-and-away basis, except for the final which was played as a single-leg game.
