The 2005–06 season was Fussball Club Basel 1893's 113th in existence and the club's 12th consecutive season in the top flight of Swiss football.

FC Basel started the season with various warm-up matches. These included teams from the Swiss lower league as well as teams from France, Croatia and the Ukraine. The FC Basel aims for the 2005–06 season were to retain the league title, win the cup and as well as to qualify for the UEFA Champions League group stage.

As Swiss champions, Basel entered the UEFA Champions League third qualifying round against German Bundesliga club Werder Bremen.

Basel's biggest signings of the 2005–06 season were defenders Daniel Majstorović and Kōji Nakata, who were brought in to replace Lyon-bound Patrick Müller and the retiring Murat Yakın. Forward Eduardo was signed permanently following his successful loan spell but Argentinian strikers Christian Giménez and Julio Hernán Rossi left the club.

Basel's priority aim for the season was to win the league championship for the third time in a row. Despite the 3-0 defeat by FC Thun in the second round, Basel started the season well and led the championship right until the last day of the league campaign. On 26 February 2006, FC Basel broke their own club record of 52 unbeaten league games at St. Jakob Park, later extending it to 59. The unbeaten home run ended on the final day of the season with a last-minute goal from Zürich's Iulian Filipescu giving Zürich their first national championship since 1980–81. A 60th straight home league match undefeated would have made Basel champions for third time in a row. The final score was 1-2 in favour of Zürich. The last minute loss of the Championship and the subsequent riots, the so-called Basel Hooligan Incident, meant that the club suffer the consequences. As well as a huge fine, the first two home games of the 2006–07 Swiss Super League season were held completely without fans, behind closer doors. The following three matches were held with just a part of the stadium capacity, without the fans from the "Muttenzer Kurve" (the eastern fan block).

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