Steve Munby will step down next August after almost five years in charge of the organisation formerly called the CfBT Education Trust.
Mr Munby said it had been "huge privilege" to be involved in the work of the Education Development Trust.
The chief executive of the charity, which provides a range of international education improvement services, added: "I am very proud of our team and the impact they make around the world."
Prior to joining the CfBT, Mr Munby had been chief executive of the National College of School Leadership and, before that director of education in Knowsley, Merseyside.
"Driving through improvements in education is a complex process and it is a huge privilege to be involved in this important work in so many different contexts," Mr Munby said.
"It is great to know that we are increasing the life chances of children through education everywhere we work”.
Philip Graf, chairman of EDT's board of trustees, said: "Steve has been an outstanding CEO and done an excellent job for the company.
"While we are very sorry to lose him, we are confident that we will find a successor of the highest calibre; work on this has already commenced”.