The 1948–49 Greek Football Cup was the seventh edition of the Greek Football Cup. The competition culminated with the Greek Cup Final, replayed at Leoforos Alexandras Stadium, on 3 July 1949, because of the previous match (19 June) draw. The match was contested by AEK Athens and Panathinaikos, with AEK Athens winning by 2–1 after extra time.
Calendar
Qualification round
First round
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Central Greece/Islands Football Clubs Association ||colspan="2" rowspan="12"
||colspan="2" rowspan="10"
|}
Second round
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Central Greece/Islands Football Clubs Association ||colspan="2" rowspan="4"
||colspan="2" rowspan="5"
||colspan="2" rowspan="3"
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Crete Football Clubs Association ||colspan="2" rowspan="2"
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Patras/Western Greece Football Clubs Association ||colspan="2" rowspan="5"
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Thessaly Football Clubs Association ||colspan="2" rowspan="3"
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Thessaloniki Football Clubs Association ||colspan="2" rowspan="6"
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Eastern Macedonia Football Clubs Association ||colspan="2" rowspan="6"
|}
*Ethnikos was zeroed due to late arrival in the match. A friendly match against Ionikos Asteras Thiva took place instead that ended 3–7.
Third round
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Central Greece/Islands Football Clubs Association ||colspan="2" rowspan="2"
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Crete Football Clubs Association ||colspan="2" |- |colspan="5" style="background-color:#D0D0D0" align=center|Patras/Western Greece Football Clubs Association ||colspan="2" rowspan="2"
||colspan="2" rowspan="2"
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Thessaly Football Clubs Association ||colspan="2" rowspan="5"
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Eastern Macedonia Football Clubs Association ||colspan="2" rowspan="2"
||colspan="2" |}
* Olympiacos Corinth won the match by, 2–3 but was zeroed due to illegal usage of football players.
**Suspended due to the withdrawal of Ionikos Astaras Thiva.
Additional round
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Central Greece/Islands Football Clubs Association ||colspan="2" |- |colspan="5" style="background-color:#D0D0D0" align=center|Crete Football Clubs Association ||colspan="2" |- |colspan="5" style="background-color:#D0D0D0" align=center|Patras/Western Greece Football Clubs Association ||colspan="2" |- |colspan="5" style="background-color:#D0D0D0" align=center|Thessaly Football Clubs Association ||colspan="2"
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Thessaloniki Football Clubs Association ||colspan="2" rowspan="4"
|}
* Aris Thiva resigned.
Fourth round
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Central Greece/Islands Football Clubs Association ||colspan="2"
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Crete Football Clubs Association ||colspan="2" rowspan="2"
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Patras/Western Greece Football Clubs Association ||colspan="2" |- |colspan="5" style="background-color:#D0D0D0" align=center|Thessaly Football Clubs Association ||colspan="2" rowspan="2"
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Thessaloniki Football Clubs Association ||colspan="2" |- |colspan="5" style="background-color:#D0D0D0" align=center|Eastern Macedonia Football Clubs Association ||colspan="2" rowspan="3"
|}
Fifth round
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Central Greece/Islands Football Clubs Association ||colspan="2" rowspan="4"
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Patras/Western Greece Football Clubs Association ||colspan="2" rowspan="2"
||colspan="2" |- |colspan="5" style="background-color:#D0D0D0" align=center|Thessaly Football Clubs Association ||colspan="2"
|-
|colspan="5" style="background-color:#D0D0D0" align=center|Eastern Macedonia Football Clubs Association ||colspan="2" rowspan="2"