It has played in the Nationalliga B from 1946–50, 1953–54, 1955–70 and 1997–2002. From 2002–2008 it played in the Nationalliga A, which was renamed to Axpo Super League. In 2008 the club were relegated to the Swiss Challenge League.
FC Thun reached for the first time the group stages of the 2005–06 UEFA Champions League, and were drawn in Group B alongside European giants Arsenal, Ajax and Sparta Prague. They started their campaign on 14 September 2005 away at Arsenal, where after equalising through Nelson Ferreira, they narrowly lost 2–1 after Dennis Bergkamp scored in the match's dying seconds. On 27 September they hosted the Czech champions Sparta Prague at their 'home' venue, the Stade de Suisse, Wankdorf in Bern, where all the club's European home matches were held, as the Lachen Stadium does not meet UEFA's prerequisites for Champions League venues. Thun's 1–0 victory thanks to Selver Hodžić's 80th minute winner propelled them into second place in the group. Following a loss to Ajax on 2 November they lost 1–0 at home to Arsenal and with Ajax beating Sparta Prague, FC Thun exited the Champions League. However Thun drew 0–0 with Sparta Prague in their last group match and qualifying for the UEFA Cup Round of 32.
Just three days prior to their UEFA Cup tie against Hamburg SV, Thun sacked their coach, Urs Schönenberger who had guided them to the Champions League group stages and was replaced by Heinz Peischl. Despite this Thun managed a surprise 1–0 over Hamburg SV in the first leg at the Stade de Suisse. However Hamburg were too strong at their home, AOL Arena, and managed to overturn the deficit, winning the second leg 2–0 (2–1 on aggregate).