Stupart was a senior inspector and probability officer at the Toronto Observatory. In 1894, he was appointed superintendent and director of the meteorological service and was appointed director of the Toronto Magnetic and Meteorological Observatory. He retired in 1929. In 1901, he was made a Fellow of the Royal Society of Canada.
He served as president of the American Meteorological Society from 1922 to 1923.
Stupart married Marion Dallas in 1886. Their son, Frederic Gustavus Stupart, was killed in World War I fighting during the Battle of the Somme on October 22, 1916.
He was a member of the Royal Astronomical Society of Canada and served as its president from 1906 to 1907.