He was sacked by AGF in 2000, though he recorded the best point-per-game score in AGF's modern history with 1.28. He was however surpassed by his two immediate successor, acting manager Kent Nielsen (1.36 PPG) as well as Peter Sørensen (1.32 PPG).[5]
Joining AaB for a second stint as manager in 2000, he was relieved of the job after a fourth place in the 2001-02 Danish Superliga, since the AaB directors "were uncertain about whether Rudbæk would be able to live up to Aalborg's ambitions for the future".[6]