The 62-year-old has signed a three-year contract to succeed Christoph Daum at Jan Breydelstadion, the Jupiler League club confirmed.
Leekens has been in charge of the national team since May 2010, leading the country to third place in Group A behind Germany and Turkey in qualifying for UEFA EURO 2012.
Club Brugge have qualified for the UEFA Champions League qualifying round next season. The former defender spent nine years at the club as a player. This will be his second spell there as a coach.