The club also took part in the 2012–13 edition of the DFB-Pokal, the German Cup, where it reached the second round and subsequently lost to Bundesliga side SC Freiburg.

[1] Due to the ongoing rebuilding of the Eintracht-Stadion, the stadium's capacity is reduced during the season.

[2] Eintracht Braunschweig started the season by winning five games in a row and taking over first place in the league on the second matchday.

[3][4][5][6][7][8] On the 31st matchday, the club secured its return to the Bundesliga after a 28-year absence with a 1–0 away win over FC Ingolstadt.

[9] Damir Vrančić scored the decisive goal from a free-kick in injury time.