To ensure the most lucrative broadcasting deals and an exciting competition, the clubs Season 1 of Mega League are pre-selected based on popularity, traditional rivalries, historical accomplishments, and many other factors. Afterwards, Mega League will employ a fair promotion and relegation system, which will allow any club from the region to reach the top levels.

To illustrate the proposed format for Mega League we can look at the Italian League System. Mega League 1 will be just like Serie A in Italy. During the season (from July to May) each club will play the others twice (a standard double round-robin system), once at their home stadium and once at that of their opponents', for a total of 38 games. The 3 lowest placed clubs are relegated to Mega League 2 (like Serie B in Italy), and the 3 top clubs from Mega League 2 are promoted in their place. The format of Mega League 2 is the same, but with 22 clubs and 42 rounds.

The current top national leagues (like Superleague Greece, First Professional Football League in Bulgaria, Liga I in Romania, Serbian Superliga, etc.) will become the third level in the new Mega League System, like Serie C in Italy. The ML Qualification Tournament between the 40 top clubs from the national leagues will determine the 5 clubs to be promoted to Mega League 2 in place of the 5 relegated.