After retiring from active football, Thomassen took on a career as a youth coach, joining Vicenza, and being appointed in charge of the Under-19 team in 2022.
On 16 March 2023, following the dismissal of Francesco Modesto, he was promoted to head coach of Vicenza in the Serie C league for the remainder of the season.
[2] Just a month later, on 11 April 2023, he guided Vicenza to win the Coppa Italia Serie C after defeating Juventus F.C.
[4] Both Gastaldello and Thomassen were dismissed from their roles on 10 November 2023, following a negative string of results in the Serie B league.
[5] In March 2024, following the appointment of Luca Gotti in charge of Serie A relegation-fighting club Lecce, Thomassen joined the Giallorossi from Salento as their new assistant coach.