Frederiksen played in SønderjyskE from 2006 to 2010. After his big breakthrough in the 2009–10 Danish Superliga, a transfer to F.C. Copenhagen on 1 July 2010 was announced, but he was supposed to continue in SønderjyskE for the 2010–11 season. Although, as Morten Nordstrand turned out to be injured for all 2010, F.C. Copenhagen and SønderjyskE agreed on 1 September 2010 to transfer Frederiksen immediately. He scored his first goal for Copenhagen in a Danish Cup game against Viby IF.