He was graduated at West Point in 1822, served as adjutant in the 1st Infantry from 1825 to 1833, and was made captain in 1836. He served in the Florida war, and was brevetted major for gallant conduct at the battle of Okeechobee. He was engaged in frontier duty in the west until the Mexican war. For gallantry at the battle of Monterey, where he was wounded, he received the brevet rank of lieutenant colonel. He was at the siege of Vera Cruz and at Cerro Gordo, and served in 1847 as aide-de-camp to General Patterson.

Allen was born in tiny West Point in Columbiana County, Ohio, and was educated in the public schools. He received an appointment to the United States Military Academy and graduated in 1836, ranking 33rd out of 49 cadets. He was assigned as a second lieutenant in the 2nd U.S. Artillery and assigned to garrison duty in various outposts.