The first MFL Cup took place during the 2023 season, featuring fifteen teams. These teams were divided into two groups: Group A, consisting of eight teams, and Group B, consisting of seven teams. Each team was drawn from the Central Zone, North, South, East, Borneo, and one State team. The inaugural match of the MFL Cup was held on March 2, 2023, where Johor Darul Ta'zim II secured a 1–0 victory over Penang at the Pasir Gudang Corporation Stadium. Although Aysar Hadi was the sole goalscorer in that match, he was not the first player to score in the MFL Cup. The honor of scoring the first goal in the tournament went to Harith Najwan of the FAM-MSN Project in a match against PDRM. Terengganu II ultimately won the first MFL Cup by defeating Johor Darul Ta'zim II 1–0 in the 2023 final.
The Malaysian Football League (MFL) introduced another change involving the MFL Cup action when the 2024–25 season will feature a one-group league format instead of the two-group format used in the 2023 MFL Cup season.
The governing body explained that the league's format change was made after receiving a request from the team and as one of the initiatives to strengthen the development of the under-23 group of players (U-23). "This format change is seen to provide more matches to the players and also as requested by the clubs to increase the readiness and exposure of the U-23 players before being absorbed into the Super League team at any time.
The MFL has also allowed a quota of 5 over-age players, including 3 foreign players in each team. "In order to increase the competitiveness and intensity of the MFL Cup competition, the quota of over-age players and foreign players in this competition will also be opened to be used according to the needs and strategies of each club ."A maximum of three foreign players and two over-age players on the pitch at any one time," said the MFL.[2][3]