1. Round
31/08/2008 Olympiakos Chersonissos - APS Zakynthos 1:2
Pyrsos FC - PAE Agios Dimitrios 4:3 pso
PAS Korinthos - Ethnikos Katerini 3:0
Anagennisi Arta - AS Rhodos 0:1
Doxa Dramas FC - Alexandropoulos 3:0
Koropi FC - Eordaikos 4:3 pso
Neos Asteras Rethymno - PAONE 4:5 pso
Niki Volou FC - Preveza 2:0
Eolikos - Lamia 0:1
AO Chaidari - Thermaikos FC 1:0
Odysseas - Keravnos Kerateas 3:2
Aias Salamina - GS Ilioupolis 0:1
Agia Paraskevi FC - Fokikos FC 0:1
Makedonikos FC - Anagennisi Giannitsa 4:2
Panetolikos - Atsalenios 3:0
AO Egaleo - Panachaiki GE 0:3
Fostiras FC - Panargiakos FC 5:4 pso
Vyzas FC - Ethnikos Filippiada 1:0
2. Round
17/09/2008 APS Zakynthos - Pierikos Katerini 2:1
Pyrsos FC - GS Kallithea 1:4
PAS Korinthos - Ethnikos Piraeus 1:2 aet
AS Rhodos - AO Kavala 0:1
Doxa Dramas FC - Agrotikos Asteras 1:2 aet
Koropi FC - Ionikos Nikea 3:2 pso
PAONE - Ilisiakos 3:4 pso
Niki Volou FC - PAS Giannina 1:2 aet
Lamia - Kalamata 2:1 aet
Odysseas - Ethnikos Asteras 0:2
GS Ilioupolis - Apollon Kalamarias 3:5 pso
AO Chaidari - Veria FC 1:4 pso
Fokikos FC - AO Kerkyra 0:1
AO Makedonikos - Anagennisi Karditsa 2:1
Panetolikos - EO Volou 4:2 pso
Panachaiki GE - AGS Kastoria 0:4
Fostiras FC - Atromitos 1:3 aet
Vyzas FC - Agrotikos Asteras 0:1
3. Round
24/09/2008 Koropi FC - Atromitos 1:2
AO Kerkyra - PAS Giannina 3:0
4. Round
28/10/2008 12:15 APS Zakynthos - Panthrakikos 0:2 aet
15:45 AO Makedonikos - PAOK Saloniki 1:2
29/10/2008 12:15 Panetolikos - AE Lárissa 0:2
12:45 Ethnikos Piraeus - Panionios GSS 0:2
15:45 Diagoras FC - Olympiakos Piraeus 2:3
30/10/2008 13:00 Apollon Kalamarias - Asteras Tripolis 0:1
11/11/2008 15:45 Ilisiakos - AEK Athen 1:2 aet
12/11/2008 12:15 Agrotikos Asteras - OFI Heraklion 1:2
12:45 GS Kallithea - Skoda Xanthi 1:3
13:00 Lamia - Panserraikos 1:2
13:00 Veria FC - Thrasyvoulos Fylis 3:1
14:30 AO Kerkyra - Levadiakos 4:2 pso
14:50 Atromitos - Aris Saloniki 1:2
15:00 Ethnikos Asteras - Ergotelis 0:2
17:00 AO Kavala - Panathinaikos 0:3
13/11/2008 13:00 AGS Kastoria - Iraklis Saloniki 2:3 aet
Round of 16
13/01/2009 14:45 Veria FC - Panionios GSS 0:0
14/01/2009 16:45 Panthrakikos - Panathinaikos 0:4
19:10 PAOK Saloniki - Aris Saloniki 0:0
15/01/2009 14:45 Ergotelis - Skoda Xanthi 0:3
20/01/2009 14:45 Asteras Tripolis - Iraklis Saloniki 2:0
21/01/2009 14:45 Panserraikos - AE Lárissa 1:0
18:00 OFI Heraklion - Olympiakos Piraeus 0:2
22/01/2009 14:45 AEK Athen - AO Kerkyra 1:0
28/01/2009 15:30 Panionios GSS - Veria FC 2:0
19:00 Aris Saloniki - PAOK Saloniki 8:9 pso
Quarter-finals
04/02/2009 17:00 Panserraikos - Panathinaikos 0:0
19:15 PAOK Saloniki - Olympiakos Piraeus 1:0
18/02/2009 14:45 Panionios GSS - Asteras Tripolis 0:1
19:30 Skoda Xanthi - AEK Athen 2:1
25/02/2009 17:00 AEK Athen - Skoda Xanthi 1:0
04/03/2009 14:00 Asteras Tripolis - Panionios GSS 1:0
17:00 Panathinaikos - Panserraikos 2:3
19:15 Olympiakos Piraeus - PAOK Saloniki 2:0 aet
Semi-finals
18/03/2009 17:00 AEK Athen - Panserraikos 3:1
19:15 Asteras Tripolis - Olympiakos Piraeus 2:2
08/04/2009 15:00 Panserraikos - AEK Athen 0:0
09/04/2009 16:00 Olympiakos Piraeus - Asteras Tripolis 2:1
Final
02/05/2009 18:30 AEK Athen - Olympiakos Piraeus 14:15 (2:0, 3:3, 4:4) pso