For Belgium, Wilmots scored 28 goals in 70 caps, his first coming in May 1990. He went to four World Cups, playing in three. After being an unused substitute in 1990, he played 54 minutes in 1994 without scoring, but scored two goals in 1998 and three in 2002, making him Belgium's leading goal scorer in World Cup history. He also scored a goal against Brazil in the last 16 match of the 2002 World Cup which was disallowed because of a "phantom foul" on Roque Júnior. According to Wilmots, the referee Peter Prendergast apologized for the error to him at half time. Wilmots was named as one of the seven reserves in the 2002 World Cup All-Star Team.