Additions
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 05/2007 |  | Manuel Riemann | GK |  | Wacker Burghausen II | Burghausen II |
| 05/2007 |  | Sergej Volkov | DF | | Wacker Burghausen II | Burghausen II |
| 01/2007 |  | Josef Laštovka | DF | |||
| 01/2007 |  | Goce Toleski | FW |  | FK Renova | FK Renova |
| 01/2007 |  | Nikolas Ledgerwood | MF |  | 1860 Munich | 1860 Munich |
| 01/2007 |  | Gino Lettieri | MA | |||
| 01/2007 | | Lukas Lechner | DF | | Wacker Burghausen II | Burghausen II |
| 01/2007 | | Timo Nagy | MF |  | Hannover 96 | Hannover |
| 12/2006 | | Alfred Arbinger | MA |  | Wacker Burghausen U19 | U19 |
| 12/2006 | | Wolfgang Riedl | AS-CO | |||
| 09/2006 | | Roland Bonimeier | MF |  | TSG Hoffenheim | Hoffenheim |
| 07/2006 |  | Markus Palionis | DF | | Wacker Burghausen II | Burghausen II |
| 07/2006 |  | Dilaver Satilmis | DF |  | SV Darmstadt 98 | Darmstadt |
| 07/2006 | | Stefan Aigner | MF |  | 1860 Munich U19 | 1860 Munich U19 |
| 07/2006 |  | Andy Nägelein | MF |  | Kickers Emden | Emden |
| 07/2006 |  | Maximilian Nicu | MF |  | SV Wehen Wiesbaden | Wiesbaden |
| 07/2006 | | Özgür Kart | FW |  | Hamburger SV II | Hamburg II |
| 07/2006 |  | John Mosquera | FW |  | SønderjyskE | SønderjyskE |
Departures
| from | Name | Pos | Team | Team | ||
|---|---|---|---|---|---|---|
| 01/2007 | | Sebastian Kneißl | MF |  | Fortuna Düsseldorf | Düsseldorf |
| 01/2007 | | Andy Nägelein | MF | | Kickers Emden | Emden |
| 01/2007 | | Wolfgang Riedl | AS-CO | | Wacker Burghausen U19 | U19 |
| 07/2006 | | Martin Forkel | DF |  | TuS Koblenz | TuS Koblenz |
| 07/2006 | | Nico Herzig | DF |  | Alemannia Aachen | Aachen |
| 07/2006 | | Robert Paul | DF |  | FC Carl Zeiss Jena | Jena |
| 07/2006 | | Denny Herzig | MF |  | SV 07 Elversberg | Elversberg |
| 07/2006 |  | Marek Kostoláni | MF | | Wacker Burghausen II | Burghausen II |
| 07/2006 | | Timo Nagy | MF | | Hannover 96 | Hannover |
| 07/2006 | | Martin Oslislo | MF |  | Wuppertaler SV | Wuppertal |
| 07/2006 | | Rafael Kazior | FW |  | Holstein Kiel | Holstein Kiel |