Mr Leekens was handed the job four months ago and started his reign with a 3-1 loss to Nigeria in the 2018 World Cup qualifying series.
He replaced Milan Rajevac who resigned following their 1-1 draw at home to Cameroon in the 2018 World Cup Qualifiers.
The Belgian tactician dumped the Greens after their exit from the African Cup of Nations where his side failed to win a game.
The Fennecs drew two and lost one in the group stage of the competition despite parading the reigning African Footballer of the Year Riyad Mahrez.
The Desert Foxes will be up against Zambia in a 2018 World Cup qualifier in August in their next competition game.
Leekens said in a statement on the AFF website, “For the good of all, I decided to quit even though I do it with heartache, and I wish all the success in the world to the national side.”