FCK won the Danish Superliga trophy in the season 2005-06. The championship was secured on May 7 after a 0–1 defeat at Fionia Park against Odense BK, but with simultaneously, AC Horsens winning 4–1 over Brøndby IF.
They won on April 6 the Royal League again, after an exciting final against Lillestrøm S.K., where Razak Pimpong scored the decisive goal in the final seconds.
FCK were knocked out of the UEFA Cup by Hamburger SV on September 29 after a very controversial refereeing performance by British Matthew Messias, giving eight yellow cards, two of those leading to a sending off, and a third direct red card, all in the last ten minutes, and giving HSV a 92nd-minute penalty kick.