Stokes, whose father worked in the Indian Civil Service, was born at Lausanne in Switzerland and educated at Trinity College, Dublin, where he obtained his MD in 1911. After serving in the Royal Army Medical Corps during the war, in which he was awarded the DSO, he returned to Dublin in 1919 as professor of bacteriology but soon moved to London, where in 1922 he became professor of pathology at Guy's Hospital.

In 1920 Stokes visited Lagos to study yellow fever. He was anxious to test the suggestion of the Japanese bacteriologist Hideyo Noguchi that yellow fever was caused by the bacillus Leptospira icteroides, but it was not until his second visit to Lagos in 1927 that he made the vital breakthrough.

Stokes succeeded, for the first time, in infecting an experimental animal (the rhesus monkey) with the disease. He went on to show that while he could pass yellow fever from monkey to monkey there was no evidence that Noguchi's bacillus was also transmitted. But before he could proceed further Stokes, who was daily handling infected monkey blood, contracted the disease and joined the growing list of bacteriologists who had fallen victim to the virus.