Thys was at the helm of the Belgian side from 1976 until August 1989. Following a six-month break, he took charge of the side again in February 1990 after Walter Meeuws was sacked.

Thys was in charge for 114 games in total, winning 50, drawing 27 and losing 37. He finally relinquished the post in May 1991.

His finest hour came when Belgium reached the last four of the 1986 World Cup in Mexico, where they lost 2-0 to Diego Maradona-inspired Argentina in Mexico City. Thys also led Belgium to the final of the 1980 European Championship. They lost 2-1 to West Germany in Rome.

He was still active at 80 in a public relations role for the Belgian Football Association and as a member of the Belgian FA's coaching school.