He graduated from University of Pittsburgh in 1915, where he also became a member of the Sigma Chi Fraternity.

He served as a Lieutenant in the 28th (keystone) Division, United States Army during the World War I and fought in the Aisne-Marne offensive July-August, 1918. He wrote "Toward the Flame" (1926), a nonfictional account of his experiences in the war.

Allen is best known for his work Anthony Adverse. He also planned a series of novels about colonial America called The Disinherited. He completed three works in the series: The Forest and the Fort (1943), Bedford Village (1944), and Toward the Morning (1948). The novels tell the story of Salathiel Albine, a frontiersman kidnapped as a boy by Shawnee Indians in the 1750s. All three works were collected and published as the City in the Dawn. Allen also wrote Israfel (1926), a biography of American writer Edgar Allan Poe.

For a period of time, Allen taught at the Porter Military Academy in Charleston, South Carolina. He also taught English at Charleston High School which at that time, although public, was only for boys. (The girls went to Memminger.) There he met and befriended DuBose Heyward.

In the 1940s he co-edited the Rivers of America Series with Carl Carmer. Allen was a good friend of Marjory Stoneman Douglas and instigated her writing River of Grass.

Allen died at his home, called the Glades, in Coconut Grove, Florida from a heart attack while in the shower, and was found by his wife Annette.