Martin Thomsen (born 6 August 1982) is a retired Danish footballer who played as a midfielder. He is currently the assistant manager of Skive IK.
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. Thomsen only played 9 minutes altogether in the Superliga, as a substitute against F.C. Copenhagen on July 21, 2001. In the summer of 2003 he was loaned to Skive IK on a one-year basis. Viborg terminated Thomsen's contract after his loan spell at Skive.
Thomsen signed with Skive IK on a permanent basis in 2004. He would stay at the club until 2013. In 2011, Thomsen scored 12 goals in the Danish second division, which was a decisive factor in Skive's surprising 4th place in the league. He was therefore awarded the Most Valuable Player-award, in front of players like Simon Makienok, Peter Graulund and Stephan Petersen.
In 2013, he was sold to his childhood club Hobro IK, where he had started his career. With this club, he promoted to the Superliga in 2014.