In 1849, Norman and four other doctors started a third medical school in Toronto called the Upper Canada School of Medicine. When a big dispute broke out over the conversion of Kings College to a secular school, the University of Toronto, Bishop John Strachan started Trinity College as a new Anglican alternative. The Upper Canada Medical Group, including Bethune, became the medical faculty of the new college. However, the medical school had difficulty in attracting enough paying Anglican students and started offering instruction to others as well. A dispute broke out with Strachan, causing the mass resignation of the medical faculty.
Bethune and many other faculty joined the Toronto School of Medicine. He taught successfully there and then returned to Trinity College in 1871. He was professor of surgery there until 1881. His career drew little recorded notice from that time until his death. His career spans an era when science separated itself from religion and government became increasingly involved in the funding of medical education.
He had a grandson, Henry Norman Bethune who also became a physician and achieved high recognition for his medical work and his activity in China with Mao Zedong's army.