In a letter to Synod members he said he will leave his post on 30 November.
Speaking about his departure, the 61 year old said: "After a succession of demanding roles I have, with my wife, concluded that the time has come for me to retire from full time work and move to a more flexible pattern of life.
"I am giving a substantial period of notice in the hope that this will facilitate a smooth and orderly transition. It is likely to take around three months for the selection process to be completed and the person chosen may then have several months' notice to serve from their present role."
The Archbishop of Canterbury, Most Revd Justin Welby has paid tribute. He said: "William has made a substantial and prodigious contribution to the work and life of the Church of England.
"For over a decade he has been unstinting in his efforts to ably lead the staff of the Council and professionally support the work of the Synod. He has been indefatigable in his service and I will personally miss him greatly."
Mr Fittall has been in the role since 2002, before then he worked in various Whitehall posts.