Hunter had been intended and educated for the Church, but on the advice of the surgeon William Cullen he turned his attention to the study of medicine. His first attempt at teaching was in 1746, when he delivered a series of lectures on surgery for the Society of Naval Practitioners. These lectures proved so interesting and instructive that he was at once invited to give others, and his reputation as a lecturer was soon established. He was a natural orator and story-teller, and he combined with these attractive qualities that of thoroughness and clearness in demonstrations, and although his lectures were two hours long he made them so full of interest that his pupils seldom tired of listening. He believed that he could do greater good to the world by "publicly teaching his art than by practising it," and even during the last few days of his life, when he was so weak that his friends remonstrated against it, he continued his teaching, fainting from exhaustion at the end of his last lecture, which preceded his death by only a few days.

For many years it was Hunter's ambition to establish a museum where the study of anatomy, surgery, and medicine might be advanced, and in 1765 he asked for a grant of a plot of ground for this purpose, offering to spend seven thousand pounds on its, erection besides endowing it with a professorship of anatomy. Not being able to obtain this grant, however, he built a house, in which were lecture and dissecting rooms, and his museum. In this museum were anatomical preparations, coins, minerals, and natural-history specimens.

Hunter's weakness was his love of controversy and his resentment of contradiction. This brought him into strained relations with many of the leading physicians of his time, notably his own brother John, who himself was probably not entirely free from blame in the matter. Hunter is said to have excused his own irritability on the grounds that being an anatomist, and accustomed to "the passive submission of dead bodies," contradictions became the more unbearable. Many of the physiological researches begun by him were carried on and perfected by his more famous brother, particularly his investigations of the capillaries, but he added much to the anatomical knowledge of several structures of the body, notably as to the structure of cartilages and joints.