The US fast food giant said it had been consensual, but Mr Easterbrook had violated company policy and shown poor judgement.
In an email to staff, the British businessman acknowledged the relationship and said it was a mistake.
"Given the values of the company, I agree with the board that it is time for me to move on," he said.
Mr Easterbrook, 52, who is divorced, first worked for McDonald's in 1993 as a manager in London before working his way up the company.
