He is currently director of the University of Toronto's Munk School of Global Affairs.
The Canadian academic, with an expertise in international law, was a postgraduate student at Cambridge in the 1980s.
Prof Toope will take over in October 2017, when the current vice-chancellor, Sir Leszek Borysiewicz, steps down.
The new Cambridge head, whose appointment will have to be approved by the university's governing body, is a former vice-chancellor of the University of British Columbia.
His academic work has specialised in human rights and international dispute resolution, and he has worked for the UN Working Group on Enforced or Involuntary Disappearances.
Prof Toope will be the 346th person to hold the office, in a role dating back to 1412.
He said: "I am thrilled to be returning to this great university.
"I look forward to working with staff and students in the pursuit of academic excellence and tremendous international engagement."
Stephen Toope has been chosen as the next vice-chancellor of the University of Cambridge.