The directors award, presented on the last day of the 61st Cannes festival, is one of the premier awards of the event and one of the highest forms of recognition that a director can receive.
In accepting his award, Ceylan said he was honoured to receive the directors prize from the Cannes jury.
I dedicate it to my beautiful country Turkey, he said.
Three Monkeys stars Yavuz Bingol, Hatice Aslan, Ahmet Rifat Sungar, Ercan Kesal, Cafer Kose and Gurkan Aydin.
It is not the first time that Ceylan has come away with a major prize from Cannes. His film Uzak (Distant) took the Grand Jury Prize and the Best Actor Prize at Cannes, while his film Iklimler (Climates) won the FIPRESCI Movie Critics Award at the 2006 Cannes Film Festival.