Network Rail said Mr Coucher’s decision was for “purely personal reasons”.
He will remain in his post over the coming months to help in the search for a successor to allow for a smooth handover.
Network Rail chairman, Rick Haythornthwaite, said: “Iain has been an outstanding leader for Network Rail both as chief executive and deputy chief executive.
“What was a company with enormous problems in 2002 is a strong and stable one today – and Britain’s rail users and taxpayers are the main beneficiaries.
“The Board and Coucher agreed that, with Network Rail one year into a five year financial settlement, now is the ideal time in our financial and regulatory cycle for Iain to hand over to a new chief executive.”
Network Rail chief executive, Iain Coucher, said: “Following three years as chief executive, and five before that as Deputy, now is a good time for me to move on. The company needs continuity of leadership throughout the next five year regulatory review period.
“Leading the thousands of dedicated railwaymen and women that make up this company has been the greatest privilege of my professional life.”
Mr Coucher earned a basic salary of £605,000 in 2009 and gave up part of his bonus.
He was previously chief executive of London Underground infrastructure company TubeLines.