 In 2005, Frederiksen was put in charge of the entire youth department of B.93, while he also worked as assistant coach to the first team which competed in the Danish 2nd Division (third highest division).In November 2005, he signed a contract as under-19 coach for Lyngby Boldklub, and he left B.93 in late 2005.Frederiksen began coaching the Lyngby Boldklub under-17 and under-19 sides beginning 1 January 2006.