The 1938–39 Panhellenic Championship was the tenth season of the highest football league of Greece.
The South Group comprised club of Athens' and Piraeus' associations and resulted as follows: The North Group consisted of clubs from Macedonian and East Macedonian associations and resulted as follows: It was the first time that teams outside Central Greece and Thessaloniki participated in the national championship.
The champions of the two groups, AEK Athens (due to a better goal ratio than Olympiacos) and Iraklis, competed in a 2-legged final for the title of champion.
From this period, the HFF established a point system of 3-2-1 in all competitions, so that there was the ability of zeroing any team that refused to take part in a match.
AEK Athens won 7–3 on aggregate.