The 2011–12 season saw Viktoria finish in third place in the league, three points behind champions Slovan Liberec, to qualify for a third consecutive Europa League campaign. Starting in the second qualifying round, the club advanced past Metalurgi Rustavi of Georgia and Ruch Chorzów of Poland to set up a play-off against the Belgian club Lokeren, in which Viktoria advanced on away goals after a 2–2 aggregate draw. The club finished first in Group B, ahead of the tournament's reigning champions Atlético Madrid. In the round of 32, Viktoria were drawn against Napoli and won 3–0 away and 2–0 at home to advance to the last 16, where they played Fenerbahçe. Viktoria lost the home leg 1–0, and in the away leg (which was played behind closed doors due to the Istanbul club's fans' recent conduct) drew 1–1, resulting in their elimination. Viktoria won the Czech league for a second time in the 2012–13 season.