In 1928 Babkin became a research professor at McGill University, Montreal, where he spent the remainder of his career. He chaired the Physiology department between 1940 and 1941, and following his retirement was invited to become Research Fellow of Neurosurgery by Wilder Penfield; a position he held until his death in 1950.
In 1950, he was elected a Fellow of the Royal Society for "his work on the digestive glands, conditioned reflexes and the cortical representation of autonomically innervated organs. He demonstrated that a) the three pancreatic enzymes are secreted in parallel, b) sympathetic and parasympathetic fibres innervate different cells in the salivary glands and c) histamine stimulates exclusively gastric parietal cells. His researches not only refuted Heidenhain's theory of "secretory" and "trophic" nerves but led to the conception of the elements of the digestive glands being activated by different nerves and hormones. Author of "Die aussere Sekretion der Verdauungsdrusen" and "Secretory Mechanism of the Digestive Glands""