Thomsen started his career playing for Valsgård IF 83, before joining his hometown side Hobro IK.

Viborg FF quickly caught notion of the midfielder, and he signed a three-year contract at the Superliga team.

In 2011, Thomsen scored 12 goals in the Danish second division, which was a decisive factor in Skive's surprising fourth place in the league.

[7] In January 2017, it was announced that he was taking up a position as player-assistant at Jammerbugt FC for a period of six months.

[9] Thomsen announced his retirement as a player in August 2018, and was instead appointed as the assistant coach to Thomas Røll at Skive.