In 1923, Macnamara became a resident doctor at the Royal Children's Hospital in Melbourne. Hospital authorities had at first been reluctant to employ her on the grounds that it had no toilet facilities for women doctors. During her time at the Children's Hospital, there was a polio outbreak. She and Burnet demonstrated that there was more than one strain of the virus, a fact that would be important in the later development of the Salk vaccine. Between 1925 and 1931 she was consultant and medical officer responsible to the Poliomyelitis Committee of Victoria, and between 1930 and 1931 was an honorary adviser on polio to official authorities in New South Wales, South Australia and Tasmania.