Bavarian Cup Bavarian Cup era Bavarian Cup era

| Season | Oberbayern | Niederbayern | Schwaben | Mittelfranken |
|---|---|---|---|---|
| 1998 | TSV 1860 München II | SV Schalding-Heining | BC Aichach | Jahn Forchheim |
| 1999 | TSV 1860 Rosenheim | SpVgg Landshut | FC Augsburg | SG Quelle Fürth |
| 2000 | FC Ismaning | SV Riedelhütte | TSV Rain am Lech | FSV Erlangen-Bruck |
| 2001 | FC Bayern Munich II | SpVgg Landshut | FC Gundelfingen | 1. FC Nuremberg II |
| 2002 | FC Bayern Munich II | SpVgg Landshut | FC Augsburg | Greuther Fürth II |
| 2003 | TSV 1860 München II | SV Schalding-Heining | TSV Aindling | ASV Zirndorf |
| 2004 | SpVgg U`haching II | SpVgg Landshut | FC Augsburg | SC 04 Schwabach |
| 2005 | FC Ingolstadt 04 | 1. FC Bad Kötzting | FC Augsburg | SC 04 Schwabach |