On 10 July 2013, Papastathopoulos made his debut for Dortmund in a pre-season friendly away to Swiss club Basel at St. Jakob-Park, along with fellow BVB debutants Pierre-Emerick Aubameyang and Henrikh Mkhitaryan. On 27 July, he won his first title with the club after entering the match as a substitute in a 4–2 win over Bayern Munich for the 2013 DFL-Supercup. On 1 November 2013, he scored his first goal for Dortmund in a 6–1 win over VfB Stuttgart in the Bundesliga.