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3-1 to Wales in the quarter-finals of Euro 2016.
The 47-year-old former Belgium international held the position for four years and managed 50 games.
The Red Devils are ranked second in the world.
Belgian FA president Francois de Keersmaecker said: "The objectives set for the Euros were not achieved. We need a new momentum."
Belgium dominated large periods of the game against Wales, and Radja Nainggolan opened the scoring. But goals from Ashley Williams, Hal Robson-Kanu and Sam Vokes dumped the Red Devils out of the competition.
Wales went on to lose to eventual champions Portugal in the last four.
There were high expectations for a Belgium side second in the Fifa world rankings and described as the "golden generation" prior to both the Euros and the 2014 World Cup.
However, they fell in the last eight of both competitions, losing to eventual runners-up Argentina in Brazil.
Wilmots scored 28 goals in 70 appearances for Belgium, and won the European Super Cup in 1988 with Belgian side Mechelen.