McCrae was born on November 30, 1872 in Guelph, Ontario, and studied medicine at the University of Toronto. While there he rose to the command of the Toronto militia, the Queen's Own Rifles, and published his first poems.
McCrae served in the artillery during the Boer War, and upon his return was appointed professor of pathology at the University of Vermont, where he taught until 1911, although he also taught at McGill University in Montreal. In 1910 he accompanied Lord Grey, the Governor General of Canada, on a canoe trip to Hudson Bay.
When World War I broke out, McCrae was appointed as a field surgeon in the Canadian artillery. He was in charge of a field hospital during the Second Battle of Ypres in 1915. McCrae's friend Alexis Helmer was killed in the battle, and his burial inspired the poem, "In Flanders Fields", which was written on May 3, 1915 and published later that year in Punch magazine.