The 1940–41 Panhellenic Championship never finished, because of the WW2. The only championships that started and went on until 28 October 1940, when the Greco-Italian War started, were the Athenian, Piraeus' and Macedonian championship. The point system was: Win: 3 points - Draw: 2 points - Loss: 1 point.

Qualification round

Athens Football Clubs Association

PosTeamPldWDLGFGAGDPtsGOUDAEKPAOATHPAGASTATRARK
1Goudi Athens3300141+1396–06–1
2AEK Athens3300122+1094–16–02–1
3Panathinaikos311143+160–02–0
4Athinaikos311157−263–2
5A.O. Pangrati311136−360–03–0
6Asteras Athens302117−651–1
7Atromitos301204−440–26–0
8Arion Kolonaki3003211−936–0

Suspended 27 October 1940, with P. Angelopoulos being the top scorer of the association with 8 goals.

Piraeus Football Clubs Association

PosTeamPldWDLGFGAGDPtsOLYPROETHNKERTHEARISARG
1Olympiacos3300130+1392–07–04–0
2Proodeftiki311185+366–2
3Ethnikos Piraeus311175+262–25–1
4Keramikos Kaminia311139−661–02–2
5Thiseas Piraeus210155045–1
6Aris Piraeus201137−43
7Argonaftis Piraeus2002311−82

Suspended 27 October 1940.

Macedonia Football Clubs Association

PosTeamPldWDLGFGAGDPtsARISPAOKIRAMENTMAKMEG
1Aris321082+682–04–0
2PAOK321096+382–25–32–1
3Iraklis310235−251–0
4MENT3102611−553–2
5Makedonikos100112−11
6Megas Alexandros100101−11

Suspended 27 October 1940.

Final round

Not held.