The 2016–17 1. FC Magdeburg season was their second season in the 3. Liga. As in the previous season, the side finished fourth overall, qualifying for the 2017–18 DFB-Pokal. In addition, Magdeburg won the Saxony-Anhalt Cup, increasing their record to 11 wins in that competition. Their run in the 2016–17 DFB-Pokal was cut short, when the team lost to eventual finalists Eintracht Frankfurt on penalties in the first round.