Born in Copenhagen, Thygesen started playing youth football for Greve Fodbold and later Brøndby IF, before getting his senior debut with Danish 1st Division (second tier) club BK Frem in the 2002–03 season.

Originally bought as a winger by Midtjylland,[2] Thygesen made his breakthrough as a central midfielder, when he scored seven goals for the club in the first half of the 2006–07 season.

[7] He made two appearances under head coach Jupp Heynckes, before the latter was fired, which meant that Thygesen had a hard time finding his way into the first team.

Thygesen made his debut for the Danish under-21 national team in November 2004, when he replaced Sebastian Svärd in the second half of the 2006 European Under-21 Championship qualification match against the Georgia under-21s.

Five days later, he was called up for the league national team, for the trip to the United States, El Salvador and Honduras in January 2007.

[14] On January 6, 2025, Thygesen was presented as the new manager of Danish 2nd Division side Nykøbing FC, where he signed a 2.5-year contract.