Three teams were relegated at the end of the 2011–12 season to the 2012–13 Football League: Doxa Drama, Panetolikos, Ergotelis.

Three teams were promoted from the 2011–12 Football League, champions Panthrakikos, runners-up Veria and the winners of a four-team play-off round Platanias.

Panthrakikos and Veria returned to top level respectively two and four years after relegation, while Platanias made their debut.

Note: Flags indicate national team as has been defined under FIFA eligibility rules.

In the play-off for Champions League, the four qualified teams play each other in a home and away round robin.