The former Racing Genk, Anderlecht and Sporting Lisbon coach has signed a contract until the end of the season, the club said on its website.
Mechelen lie 13th in the 16-team Belgian league but are just three points above the relegation zone.
Vercauteren, 57, will take charge of his first game against champions Anderlecht at home on January 19.
He replaces Harm van Veldhoven, who was fired last week.
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