According to L. Sprague de Camp, Pratt was born near Tonawanda , New York, and attended Hobart College for one year. During the 1920s he worked for the Buffalo Courier-Express and on a Staten Island newspaper. In 1926, he married Inga Stephens Pratt, an artist. In the late 1920s he began selling stories to pulp magazines. Again, according to de Camp's memoir, when a fire gutted his apartment in the 1930s he used the insurance money to study at the Sorbonne for a year. After that he began writing histories.
Wargamers know Pratt as the inventor of a set of rules for civilian naval wargaming before the Second World War. This was known as the "Naval War Game" and was based on a wargame developed by Fred T. Jane involving dozens of tiny wooden ships, built on a scale of one inch to 50 feet. These were spread over the floor of Pratt's apartment and their maneuvers were calculated via a complex mathematical formula. Noted author and artist Jack Coggins was a frequent participant in Pratt's Navy Game, and De Camp met him through his wargaming group.
Pratt established the literary dining club known as the Trap Door Spiders in 1944. The name is a reference to the exclusive habits of the trapdoor spider, which when it enters its burrow pulls the hatch shut behind it. The club was later fictionalized as the Black Widowers in a series of mystery stories by Isaac Asimov. Pratt himself was fictionalized in one story, "To the Barest", as the Widowers’ founder, Ralph Ottur.
He was also a charter member of The Civil War Round Table of New York, organized in 1951, and served as its president from 1953-1954. In 1956, after his death, the Round Table's board of directors established the Fletcher Pratt Award in his honor, which is presented every May to the author or editor of the best non-fiction book on the Civil War published during the preceding calendar year.
Aside from his historical writings, Pratt is best known for his fantasy collaborations with de Camp, the most famous of which is the humorous Harold Shea series, was eventually published in full as The Complete Compleat Enchanter (1989, ISBN 0-671-69809-5). His solo fantasy novels The Well of the Unicorn and The Blue Star are also highly regarded.
Pratt wrote in a markedly identifiable prose style, reminiscent of the style of Bernard DeVoto. One of his books is dedicated "To Benny DeVoto, who taught me to write."
Several of Pratt's books were illustrated by Inga Stephens Pratt, his wife.