Born in Wilmington, Delaware, Gillis was appointed midshipman in 1825. He served with distinction in the Mexican-American War at the capture of Tuxpan. In 1853-1854, he sailed with Commodore Matthew C. Perry"s expedition to open Japan to the West.
During the Civil War he commanded Monticello, Seminole and Ossipee in the Union blockade, and subsequently was on duty at New York until retiring in 1866.
Commodore Gillis died in the city of his birth. The destroyer United States Ship Gillis (Doctor of Divinity-260) was named for him and Rear Admiral James Henry Gillis.