Lee was licensed as a preacher in 1807, and after acting for a few months as pastor of a Presbyterian chapel in London he was ordained as minister of Peebles. In 1812 he was appointed Professor of Church History at St Mary's College, St Andrews, and was there chosen rector of the college. In 1820 he became Professor of Moral Philosophy in King's College, Aberdeen, but his lectures there were mostly delivered by a deputy. He continued to lecture in St Andrews, intending to travel regularly between the two, however, he had a change of heart following a near-fatal accident when his stage-coach overturned en route to Aberdeen.