The Greek Cup 1938–39 was the third edition of The Greek Football Cup, or Greek Cup for short.
The competition culminated with the Greek Cup Final, held at Nikos Goumas Stadium, Athens on 28 May 1939. The match was contested by AEK Athens and PAOK, with AEK Athens taking the title 2–1.
1 The match abandoned at 40' while AEK Athens gained 2-1. They won the match in cards.
The 3rd Greek Cup Final was played at the Apostolos Nikolaidis Stadium, Athens.