On 26 April 2017, helped Borussia Dortmund to a 3–2 win over Bayern Munich and their fourth consecutive DFB-Pokal final. On 20 May 2017, Papastathopoulos reached 100 appearances with Dortmund in Bundesliga in a home game against SV Werder Bremen and secured automatic qualification to the group stage of next season's UEFA Champions League. On 27 May 2017, in his fourth DFB-Pokal final in a row, Borussia Dortmund claimed a first DFB-Pokal win since 2012 as Pierre-Emerick Aubameyang's penalty defeated Eintracht Frankfurt 2–1.