He won the silver medal at the 2006 European Badminton Championships in men's doubles, with Mathias Boe. Two years later he won the bronze medal at the 2008 European Badminton Championships in mixed doubles with Helle Nielsen. In 2010, Mogensen and Boe won the titles at the Denmark Super Series, French Super Series and the Super Series Final held in Taipei. One year later Mogensen and Boe won the All England Super Series. After that they won the Li Ning China Open 2011 and the Li Ning BWF World Superseries Finals 2011. In 2012, Mogensen and Boe won the silver medal in men's doubles at the Olympics in London. In March 2015, Mogensen and Boe again won the All England Super Series.