Allen was born in Sharon Township, Michigan and attended the district and select schools. He graduated from the State normal school (now Eastern Michigan University) in 1864. After graduating near the end of the American Civil War, Allen enlisted and helped to raise a company for the Twenty-ninth Regiment, Michigan Volunteer Infantry. He was commissioned first lieutenant in September 1864 and later, captain. He mustered out with his regiment in September 1865.

Allen was graduated from the law school of University of Michigan at Ann Arbor in March 1867 and was admitted to the bar. He commenced practice in Ypsilanti. He became assistant assessor of internal revenue in 1869 and prosecuting attorney of Washtenaw County in 1872. He was alderman of Ypsilanti 1872-1874 and was elected to the Michigan State House of Representatives in 1876 and again in 1878, at which time he was elected speaker pro tempore. He was mayor of Ypsilanti in 1880 and was appointed United States Indian agent for Michigan in August 1882, serving until December 1885.

Allen lost his first election for the United States House of Representatives in 1884. In 1886, Allen was elected as a Republican from Michigan's 2nd District for the Fiftieth and Fifty-first Congresses, serving from March 4, 1887 to March 3, 1891. He was an unsuccessful candidate for reelection in 1890 to the Fifty-second Congress.

After leaving Congress, Allen resumed the practice of law and was a member of the State board of agriculture 1897-1903 and was again mayor of Ypsilanti in 1899 and 1900. He was a member of the State soldiers’ home board 1903-1909. Allen died in Ypsilanti and is interred in Highland Cemetery there.