Luke McClelland, a former head of Aquinas College for almost three years, and former operations manager at Selwyn College, will take over from interim warden Ashley Day, who retires on November 14.
The change of warden comes as the residential college for university students is mired in a debate over whether it should be sold by the Anglican Church.
The church moved at a recent synod to allow the sale at the direction of the Diocesan Council.
That will be discussed at a council meeting next week.
The board recently voted against a memorandum of understanding between Selwyn and the University of Otago.
There has been a trend for colleges run by churches to move from church control to that of the university.
Asked why a university employee had been chosen, Selwyn College board of governors chairman the Rev Aaron Douglas said it was decided, due to "significant churn within the board and with a lot of potential change coming" a known operator was needed.
"We felt that doing our own recruitment process may not give us that result."
Mr McClelland was on a fixed term, paid by the college, which would be invoiced monthly by the university.
"Our desire in seeking this appointment was to ensure a long-term appointment for the stability of Selwyn."
Mr McClelland’s career has included roles in independent organisations in the health and social sector, which included being operations manager at the Otago Youth Wellness Trust.
He has a bachelor of science degree from the University of New England in Australia, a postgraduate diploma in environmental science from the University of Queensland, a postgraduate diploma in education from Massey University, and a diploma in business administration from the University of Otago.
Mr McClelland said there was something "quite energizing" about Selwyn that left a strong impression on him.
He said during his time at both Selwyn and Aquinas he had discovered the importance of collegiate residential living, and their thriving communities.
"It is quite a privilege, really, to work alongside dedicated staff and be part of that transition in a young person’s life towards independence."