De Klerk joined Toronto FC on 6 January 2011 as First Assistant Coach along with former Ajax colleague Aron Winter who became Head Coach/Technical Director.
[6] In September 2013, after two months of managing Dutch Topklasse side Ter Leede, he became technical director at Dalian Aerbin F.C.
[7] In November 2014, he was appointed the Technical Director for York Region Shooters of the Canadian Soccer League.
[10] In the summer of 2023, he was reunited with de Boer once more and joined his coaching staff as an assistant for Al Jazira in the United Emirate's Pro League.
[12][13] After one match his caretaker spell with Al Jazira ended as the club sign Mirel Rădoi in the winter of 2024.