The 2009–10 SV Werder Bremen II season started on 25 July 2009 against Rot-Weiß Erfurt and finished on 8 May 2010 against Erzgebirge Aue.

[1] Osnabrück won the match 1–0 with a goal from the penalty spot from Matthias Heidrich.

[1] Werder Bremen II won the match 1–0 with a goal from Torsten Oehrl.

[6] Onur Ayık, Torsten Oehrl, and Pascal Testroet scored for Werder Bremen II.

[1] Jahn Regensburg won the match 1–0 with a goal from Anton Shynder.

[1] Kickers Offenbach won the match 1–0 with a goal from David Ulm.

[12] Pascal Testroet scored two goals for Werder Bremen II.

[12] Orlando Smeekes and Salvatore Amirante scored for Carl Zeiss Jena.

[1] Werder Bremen II won the match 2–0 with two goals from Torsten Oehrl.

[14] Pascal Testroet scored two goals for Werder Bremen II.

[1] Werder Bremen II won the match 1–0 with a goal from Onur Ayık.

[18] Addy-Waku Menga scored two goals for Werder Bremen II.

[24] Tobias Kempe scored two goals for Werder Bremen II.

[24] Uwe Hünemeier scored from the penalty spot for Burussia Dortmund II.

[1] Werder Bremen II won the match 1–0 with a goal from Nicolas Feldhahn.

[29] Orlando Smeekes and Melvin Holwijn scored for Carl Zeiss Jena.

[1] Dynamo Dresden won the match 1–0 with a goal from Robert Koch.

[1] Eintracht Braunschweig won the match 3–0 with goals from Deniz Doğan, Damir Vrančić, and Marco Calamita.

[1] Stuttgart II won the match 3–0 with goals from Tobias Rathgeb, who scored from the penalty spot, Julian Schieber, and Sven Schipplock.

[1] Wehen Wiesbaden won the match 2–0 with goals from Dominik Stroh-Engel and Aykut Öztürk.

[1] Werder Bremen II won the match 3–0 with goals from Timo Perthel, Sandro Wagner, and Onur Ayık.

[38] Deniz Yılmaz and Saër Sène scored for Bayern Munich II.

[39] Nicolas Feldhahn and Tobias Kempe scored for Werder Bremen II.