Thøgersen made his senior debut with BK Frem in 1989, but left the club when they were relegated in 1993. He moved to Brøndby IF in the top-flight Danish Superliga championship, and helped the club win the 1994 Danish Cup trophy from his position as forward. From 1996 to 1998, he was a part of the Brøndby team which won three Superliga titles in a row. In 1998, he moved abroad to play for English club Portsmouth in the secondary English 1st Division league. Initially playing as a defender, he was eventually moved into the attacking midfielder position. He played a total of 119 games for Portsmouth until 2002, when he returned to end his career with childhood club Frem.