Born in Albemarle County, Virginia, around 1842, Henry Lee enlisted in the Union army on April 30, 1864, near Boston, Massachusetts. According to his service records, he was 5 feet, 5 1/2 inches tall, with black hair, black eyes, and a black skin complexion, and he worked as a laborer. Lee enlisted for a period of three years, and on May 5, 1864, he mustered into the 5th Massachusetts Colored Cavalry Regiment as a private in Company M near Readville, Massachusetts.
The 5th Massachusetts Colored Cavalry performed a number of important tasks during the war. They performed garrison duty in City Point, Virginia, took part in the Siege of Petersburg, and served as prisoner-of-war escort guards in Point Lookout, Maryland. Lee developed an illness while stationed at Point Lookout, and he was admitted to the hospital in August 1864. When Confederate General Robert E. Lee surrendered in April 1865, the army moved the 5th Massachusetts Colored Cavalry to Clarksville, Texas. That August, Lee helped build the United States Military Rail Road near Boca Chica, Texas. Lee mustered out of service on October 31, 1865, near Clarksville, Texas. He never filed a pension, and his whereabouts after the war remain unknown.