Walker will be replaced in a newly-created role of director of planning and place shaping by Deirdra Armsby, who has worked as the council’s director of place shaping for the past 14 months.
In a statement, the council said that Walker had decided to leave the council "to pursue other interests".
It said: "John has made a positive contribution during his time here and we wish him well for the future."
Walker, who previously served as the council's head of development planning services, is a member of the Royal Town Planning Institute, the Planning Officers Society (POS), developer body the Major Developers Group, and architectural appreciation society the Architecture Club.
He has participated in a number of government review boards, including the 2003 Barker Review of housing supply, the 2008 Killian Pretty Review on the planning application system, the Housing Standards Review, and the sounding board for the permitted development rights review.
Other government work includes a POS and Ministry for Housing, Communities and Local Government review on underground extensions; the government’s 2017 housing white paper; the review of daylight and sunlight standards, including rights of light; along with telecoms, mobile and broadband reviews.
Armsby joined Westminster in October 2017 after serving in various roles at the London Borough of Newham, including head of planning and director of regeneration and planning.
Westminster City Council chief executive Stuart Love said: "In her 14 months as director of place shaping, Deirdra has already played a key role in a number of high-profile projects, most recently in leading the development of our plans for the Oxford Street District.
"In her new role as director of planning and place shaping, she will be responsible for making sure our residents are at the heart of every aspect of the council’s planning process, as well as changing the way development in the city is managed."
Last October, the council announced plans for a shake-up of its planning service that included allowing members of the public a right to speak at planning meetings and a clampdown on hospitality from developers. It followed a review in the wake of the councillor Robert Davis hospitality controversy.