On 8 February 2017, in a DFB Pokal home win on penalties' game against Hertha Berlin, Papastathopoulos' two quickfire (in a minute) bookings for dissent saw Dortmund finish extra time with 10 men before Fabian Lustenberger, Vladimír Darida and Salomon Kalou all erred from the spot, rendering Christian Pulisic's miss irrelevant. On 25 February 2017, Dortmund made three changes from last weekend's 3–0 win over VfL Wolfsburg and it was two of those, Papastathopoulos and Raphaël Guerreiro, who combined to open the scoring in the 13th minute in a 3–0 away win against SC Freiburg. Papastathopoulos looked to be offside as Guerreiro swung in a free-kick from the right, which the Greece defender met with a header planted inside the right-hand post.