Held by the British as an enemy alien after the outbreak of World War II, Fackenheim was sent to Canada in 1940, where he was interned at a remote internment camp near Sherbrooke, Quebec. He was freed afterward and served as the Interim Rabbi at Temple Anshe Shalom in Hamilton, Ontario, from 1943 to 1948. After this he enrolled in the graduate philosophy department of the University of Toronto and received a PhD from the University of Toronto with a dissertation on medieval Arabic philosophy (1945) and became Professor of Philosophy (1948–1984). He was among the original Editorial Advisors of the scholarly journal Dionysius. In 1971, he received an honorary doctorate from Sir George Williams University, which later became Concordia University.