He was born in Brandon, Mississippi, and was the son of Colonel Joseph McAfee Jayne, and graduated from the United States Naval Academy in 1882. During the Spanish-American War, he commanded the (TB-4) USS Rodgers in the naval blockade. During the first world war, he was promoted to Rear Admiral and commanded the naval base at Pensacola, Florida.
In 1901, he was briefly acting-Commandant of American Samoa. From 16 October 1911 until 11 February 1914 he was the Superintendent of the United States Naval Observatory, serving with the rank of Captain.