Last week talks between Mr Leekens and the Belgian FA broke down on disagreement about whether the coach could train a soccer club at the same time as being Belgium coach.
Afterwards, Leekens had regrets and contacted the FA again.
Leekens now gets the job of getting Belgium to the European Championships in Poland and Ukraine in 2012.
He succeeds the Dutchman Dick Advokaat.
Leekens will be stepping down from his post at KV Kortrijk. His plans of joining Lokeren as their new coach have been shelved.
The 60-year-old has an impressive soccer career. He started as Cercle Brugge coach in 1984. He has worked for Anderlecht, Club Brugge and AA Gent just to name a few. He coached the Red Devils on a previous occasion from 1997 until 1999.
He has also worked abroad as the coach of Trabzonspor of Turkey, Roda JC of the Netherlands and more recently Al-Hilial of Saudi Arabia.
In 1990 he won the Belgian championship title with Club Brugge. He won the Belgian Cup twice: once in 1985 with Cercle Brugge and again in 1991 with Club Brugge.