The decision comes three months before the start of the new Allsvenskan season, and almost two months after AIK finished the 2025 campaign in seventh place, four points and four places shy of European qualification.
League leaders after nine rounds of matches, the Solna side were still in third place with five matches to go, but a run of one win in seven to end the season saw them slide down the table.
AIK are yet to name a replacement, with players due in to start preseason training on Wednesday 7th January.
"When we now choose to change head coach, it is because we believe that the team and the club will be better with a different leader in the coming years," said AIK's director & CEO, Fredrik Soderberg, in a statement.
Thomassen left Norwegian side Fredrikstad to take over at AIK in July 2024 following the resignation of Henning Berg with the club sitting in eighth place. The Faroese oversaw a turnaround in form and guided Gnaget to third place and UEFA Conference League qualification.
"Mikkjal came to a team in great need of structure and organisation. It ended with a historically strong recovery in the autumn of 2024. For that, he should have all our respect and gratitude," Soderberg's statement read.
Capped 13 times for the Faroe Islands in his playing days before making his way in coaching in his homeland, the AIK job was Thomassen's first in Swedish football. He left a heartfelt message to the fans on the club's website, beginning:
"Thank you so much for the journey we had together. Thank you for giving me the opportunity to be a part of AIK for a while. It has been an honour and a responsibility that I have taken on with everything I have, every second I have had to serve you."