Sir Bob starts his new role as Permanent Secretary at the Department for Communities and Local Government on November 1.
Agency chiefs have now launched a search for his successor and an interim appointment will be made shortly with one of the current directors filing the role on a temporary basis.
HCA chairman Robert Napier said: “Bob has literally lived and breathed the HCA since he was appointed just over two years ago, and along with the hard work and commitment of all our staff he has played a major part in our success to date.
“Looking forward we have a continuing and evolving role, as well as a business to run as usual, and over the coming months we will continue to deliver against our current programmes while we shape our new way for doing business.
“I am pleased that Government recognises that the key role that the HCA has to play in helping to shape local places, and that our staff have the necessary skills and expertise to adapt to our changing world.”