The 2012–13 season is Panionios Gymnastikos Syllogos Smyrnis' 122nd season in existence and its 52nd in the top tier of the modern Greek football league system.

This season marks the managerial debut of Dimitrios Eleftheropoulos.

The club's U17 and U20 squads will compete in their respective leagues.

As of February 2013 Fostiras 2-2 Panionios.

Fostiras won on away goals.