"Kevin Hassett, who has done such a great job for me and the administration, will be leaving shortly. His very talented replacement will be named as soon as I get back to the US. I want to thank Kevin for all he has done - he is a true friend," Trump said in a tweet on Sunday.
In an interview on Sunday night, Hassett said that he had discussed the move with the President last week and that it was not related to trade policy or any other contentious issue in the White House, reports The New York Times.
"It's just normal, circle-of-life kind of things," Hassett said. "It has nothing to do with any policy disagreements. The president and I are quite friendly."
He said two years was historically the normal tenure for a chairman of the council, and "really an important part of the institution".
Hassett added that he did not know what his next move would be. "It makes me sad to leave," he said.
Hassett was an economist at the American Enterprise Institute, a conservative think-tank in Washington, when Trump chose him to serve as the administration's top academic economist.
He had advised Mitt Romney, the 2012 Republican nominee, during his presidential run.
Hassett's research has long focused on the potential to expand economic growth - and middle-class earnings - by cutting corporate tax rates.
( With inputs from IANS )