1st(1st leg) FC Slovan Rosice - Slovan Liberec 1:4 (1:3)
2nd (2nd leg) Slovan Liberec - FC Slovan Rosice 3:0 (1:0)
1st(1st leg): 17/10/2012 15:00 2nd (2nd leg): 31/10/2012 16:00 Winner: Slovan Liberec
1st(1st leg) HFK Třebíč - 1. FC Slovácko 0:2 (0:0)
2nd (2nd leg) 1. FC Slovácko - HFK Třebíč 2:0 (0:0)
1st(1st leg): 31/10/2012 13:30 2nd (2nd leg): 28/11/2012 16:00 Winner: 1. FC Slovácko
1st(1st leg) FK Dukla Praha - Sigma Olomouc 0:1 (0:1)
2nd (2nd leg) Sigma Olomouc - FK Dukla Praha 2:2 (1:2)
1st(1st leg): 31/10/2012 17:00 2nd (2nd leg): 28/11/2012 16:00 Winner: Sigma Olomouc
1st(1st leg) FK Ústí nad Labem - FK Baumit Jablonec 1:7 (1:3)
2nd (2nd leg) FK Baumit Jablonec - FK Ústí nad Labem 5:0 (4:0)
1st(1st leg): 06/11/2012 13:00 2nd (2nd leg): 27/11/2012 15:00 Winner: FK Baumit Jablonec
1st(1st leg) FK Fotbal Třinec - FK Mladá Boleslav 1:1 (0:0)
2nd (2nd leg) FK Mladá Boleslav - FK Fotbal Třinec 3:0 (0:0)
1st(1st leg): 06/11/2012 13:00 2nd (2nd leg): 28/11/2012 14:30 Winner: FK Mladá Boleslav
1st(1st leg) TJ Jiskra Domažlice - FK Teplice 0:2 (0:0)
2nd (2nd leg) FK Teplice - TJ Jiskra Domažlice 2:1 (2:0)
1st(1st leg): 07/11/2012 13:00 2nd (2nd leg): 28/11/2012 16:00 Winner: FK Teplice
1st(1st leg) Vysočina Jihlava - AC Sparta Praha 1:1 (1:1)
2nd (2nd leg) AC Sparta Praha - Vysočina Jihlava 3:2 (1:1, 1:1) pso
1st(1st leg): 29/11/2012 16:00 2nd (2nd leg): 05/03/2013 17:00 Winner: AC Sparta Praha
1st(1st leg) FC Hradec Králové - Viktoria Plzeň 2:1 (0:1)
2nd (2nd leg) Viktoria Plzeň - FC Hradec Králové 1:0 (1:0)
1st(1st leg): 29/11/2012 16:30 2nd (2nd leg): 23/03/2013 16:00 Winner: Viktoria Plzeň