Howard was born to Ossian Gregory Howard, a lawyer, and Lucy Denham Thurber on 11 June 1857. Soon after, they moved to Ithaca, New York. He attended Ithaca Academy. His interests in insect collecting led him and his friends to found the Ithaca Natural History Society to meet and discuss papers and insects. While collecting one day, he met John Henry Comstock, who invited him to his lab at Cornell University.
He enrolled in Cornell in September 1873 and initially studied civil engineering, but he soon switched to natural history and also took various language courses. He joined Comstock's lab.
He graduated from Cornell University in June 1877. He worked with Burt Green Wilder and Simon Henry Gage and received a masters at Cornell. In the 1880s, he also attended Columbian College (now George Washington University) for medicine, although he didn't complete it.
In July 1878 he was employed by the U.S. Department of Agriculture as an entomologist, and eventually became chief of the Bureau of Entomology in 1894. He held the position until 1 October 1927. He continued to consult the Bureau until officially retiring on 30 June 1931. He worked on the systemics of the parasitic Hymenoptera, biological control, and medical entomology of mosquitoes and flies.
He was the editor of Insect Life, lecturer on entomology at several colleges and universities, and a contributor to reference books on the subject of entomology. He was made permanent secretary of the American Association for the Advancement of Science, honorary curator in the United States National Museum, and consulting entomologist of the Public Health Service. He was elected to the National Academy of Sciences in 1916
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