Cole was a lecturer in zoology at the University of Liverpool from 1897 until 1906, when he became Professor of Zoology at the University of Reading, the first holder of the post. He then began setting up the Cole Museum of Zoology, encouraging overseas visitors to the Department to donate specimens. He remained at Reading until retiring in 1939, but carried on writing in retirement. He wrote in particular on comparative anatomy and the history of zoology, after his early work on the morphology of fish. His works included a "History of Protozoology" (1926), "Early Theories of Sexual Generation" (1930) and a "History of Comparative Anatomy from Aristotle to the Eighteenth Century" (1944).