Allen was born in Indiana in 1816. After beginning his career as a school teacher, he moved to Portland, Maine to study law. He was admitted to the Maine bar in 1844, becoming the first licensed African-American lawyer in the United States. He became a justice of the peace in Massachusetts in 1848, and was again the first African-American to do so. He practiced law in Boston before moving to South Carolina in 1868. He was admitted to the South Carolina Bar in November 1869 and joined in partnership with William Whipper and Robert Brown Elliott. Their law firm in Charleston was likely the first African American law firm in the nation. At age 55 he was elected by the General Assembly to succeed George Lee as judge of the Criminal Court in Charleston. He remained on the bench until the Inferior Court was abolished in 1874. Allen then served as a clerk in the Second Auditor's office of the Treasury Department from 1874 to 1876. He was a probate judge for Charleston County from 1877 to 1878 before leaving South Carolina for Washington, D.C. There he worked as an attorney for the Land and Improvement Association. He died in Washington on October 15, 1894.