Howard was born in Lexington, Kentucky (then part of Virginia) and graduated in 1797 from the College of William & Mary. He was elected to the Kentucky General Assembly in 1800. He served in the 10th and 11th Congresses from Kentucky from 1807 until April 10, 1810. One week later, on April 17, 1810, James Madison appointed him Governor of the Louisiana Territory (the Louisiana Purchase district north of modern-day Louisiana), which was later renamed as the Missouri Territory in June 1812.
He resigned his post during the War of 1812 to become brigadier general of the Eighth Military Department. During the conflict he and Nathan Boone (Daniel Boone's youngest son) attacked Sac and Fox positions in Illinois and established Fort Clark by Peoria, Illinois.
He fell ill on the way back and died September 18, 1814 in St. Louis, Missouri. His original burial location is unknown, although likely somewhere in downtown St. Louis. He was moved to the Old Grace Church Graveyard just north of downtown St. Louis (11th and Warren Street) sometime between 1817 and 1844. He was then (allegedly) reinterred in Bellefontaine Cemetery sometime after 1851. However, the cemetery has no record of Howard's body; therefore, the true location of his body remains a mystery.
Benjamin Howard is the namesake of Howard County, Missouri.