Mogensen started his coaching career at Horsens HK, where he was from 2008 to 2010. He was then the head coach for SK Aarhus from 2011 to 2013.[2]
From 2013 to 2016 he was the of the Norwegian team Byåsen HE. He has won two silver medals with in the Postenligaen in 2013-14 and 2014-15. In 2016 he was named Coach of the Year in Norwegian handball for these results.[3]
Afterwards he was the head coach at København Håndbold from 2016-2022.[4] In 2016-17 he reached the final of the Danish Championship, where they lost to Nykøbing Falster HK.[5] The same year he was named Danish Women's Coach of the Season.[6] The year after he won the Danish Championship in 2018, which was the first ever for the club.[7]
He then became the coach of Turkish club Kastamonu GSK, where he sign a one year contract. He was however fired already in February 2023 due to poor results in the EHF Champions League.[8] He then returned to Denmark, and became the assistant coach at SønderjyskE Håndbold's men's team for the rest of the season.[9] Only a week later, it was announced that he had signed a contract to become the head coach of HH Elite, the same club he started his career at, which had in the meantime had a new name. He signed a three year contract with the club.[9]
In June 2023 he became the coach of the Faroese women's national handball team as well as the head coach of HH Elite.[10]
He qualified the Faroese national team for the 2024 European Women's Handball Championship in Hungary, Switzerland and Austria, placing 17th overall.[11] This was the first time Faroe Islands participated in a major international tournament.[1] A year later he led the team to the 2025 World Women's Handball Championship, the first ever World Cup for The Faroe Islands.[12][13] Here they managed wins over Spain and Paraguay, as they advanced from the preliminary groups and recorded their first ever win at a major international tournament.[14]
