The 2012–13 FC Basel season is the 120th season in club history and the club's 18th consecutive season in the top flight of Swiss football. Basel started their season with various warm-up matches against teams from Switzerland, Romania and Germany. Their 2012–13 Swiss Super League season began on 13 July with the away tie against Servette FC and they started in the 2012–13 Swiss Cup first round on 15 September with the away game against FC Amriswil. Basel entered the Champions League in the qualifying phase and were drawn against Estonian club Flora Tallinn. This and the following qualifying round were overstood, however in the play-off round Basel lost both games against CFR Cluj and were knocked out.

Following a poor start to the season it was announced on 15 October 2012 that Vogel had been replaced by Murat Yakin as manager Following the out in the Champions League Basel played in the Europa League group stage and were drawn into Group G along with Sporting Clube de Portugal, K.R.C. Genk and Videoton FC. They finished the Group in second position and advanced to the knockout phase round of 32. Here they were drawn against the Ukrainian Premier League team Dnipro Dnipropetrovsk. Basel won 3–1 on aggregate. In the round of 16 they were drawn against Zenit St. Petersburg and, despite being the underdogs, Basel advanced by winning 2–1 on aggregate. Thus they qualified for the quarter-finals and were drawn against Tottenham Hotspur, whom they beat 4-1 on penalties after a 4-4 aggregate draw to progress to the semi-finals. The draw for the semi-final matched Basel against the reigning UEFA Champions League holders Chelsea.

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