Mr Woodhouse took on his role at the private hospital in Dunedin's Maori Hill in 2001, taking over from the then chief executive, Sister Mary Lucia.
Among his achievements while at the hospital is overseeing a $10 million expansion designed to increase elective surgery capacity by 40% in the next 10 years.
Last week, he tendered his resignation in order to concentrate on campaigning full time for this year's general election.
Mr Woodhouse said the past few weeks had been challenging in terms of balancing his increasing work as a candidate while being at the hospital.
"I am sad to be leaving the hospital. It has been my privilege to lead this outstanding Dunedin icon."
Mr Woodhouse looks assured to enter Parliament as a National Party list MP after being ranked 49th on the party list.
On paper, National has to poll above 41% for him to become the list MP based in Dunedin.
But several candidates ranked below him are likely to win electorate seats so, to be safe, National would have to poll 43% for him to become an MP.
Mercy will advertise for a chief executive in a few of weeks.
