The contractor adopted a simplified structure last year and Wainwright has decided his current role is no longer broad enough to make the best use of his experience and wider capabilities.
Wainwright joined Willmott Dixon in December 2015 from Byrne Group where he was interim finance director.
Prior to that he was financial director at Laing O’Rourke.
Group Chief Executive Rick Willmott said: “The Board has enjoyed a great working relationship with Philip over the last three years and much has been achieved in that time.
“We fully understand Philip’s decision and appreciate his candour and openness around his wish to move on and wish him every success in his future endeavours.”
Wainwright’s departure sees current Chief Financial Officer Graham Dundas promoted to the Willmott Dixon Holdings Board.
Willmott said: “Graham has benefitted from Philip’s mentoring over the last couple of years and is ideally placed to make a seamless transition to the board.
“He carries huge respect in the business, with our banking partners, auditors and sureties alike. I look forward to working even more closely with him at board level.”
Wendy McWilliams has also been appointed as a director.
McWilliams has been Company Secretary and Lawyer for over fifteen years.