Marmion began his medical career at the Public Health Laboratory Service (PHLS) as a trainee in pathology; he was seconded in this position to Cambridge and Colindale, working in the virus reference laboratory at the latter. In 1951, he was awarded a Rockefeller Fellowship allowing him to travel to Melbourne, Australia, and work at the Walter and Eliza Hall Institute of Medical Research, where he studied Murray Valley encephalitis virus and respiratory viruses alongside Macfarlane Burnet. Marmion returned to the UK in 1952, joining Michael Stoker's Q fever research group at Cambridge University. He moved to Leeds as the head of the new PHLS virus laboratory in 1955. At Leeds, he published the first description of Q fever endocarditis and co-authored a paper with Leonard Hayflick identifying the cause of Mycoplasma pneumonia.
