He was born in 1835 and graduated from Bowdoin College in the class of 1858. Two years later he was admitted to the practice of law before the Knox county bar, and once formed a partnership with Lysander Hill and opened on office in Thomaston.

The practice of his profession was followed but a short time. The smouldering fires of rebellion broke over the nation and Mr. Cilley was one of the first men to spring to his country's call. In the early part of 1861 he enlisted one hundred and fifty men and his own name headed the list of volunteers. It was intended that these men should form a light battery and H. B. Humphrey of Thomaston, offering to give the six guns required, provided that the state would complete the equipment of the battery. The War Department declined the offer on the ground that infantry only was needed at that time. When, however, it was known that cavalry also was to be raised in Maine, Mr. Cilley enlisted, and his name stands first on the rolls of the First Maine Cavalry under date Sept. 3d, 1861. He was subsequently made captain of Co. B, raised by him in the counties of Knox and Waldo, of which be remained in command until he was severely wounded in his right arm and shoulder, and taken prisoner at Middletown, Va., during the retreat of Gen. Banks from the Shenandoah Valley, May 24th, 1862. A short time after this misfortune, he received the commission of major bearing date April 14th, 1862.

After the war he returned to Maine where he was married to Caroline Abigail, daughter of Warren and Sophia (Thurber) Lazell of Brooklyn, N. Y., 10 October 1866, and resumed practice at Rockland. He was a member of the state legislature in 1867; deputy collector of customs, 1867-71; a member of the city council 1873-75; adjutant-general of Maine, 1875-77; and commissioner of the U. S. circuit court from 1867-80. His published works include orations and addresses, a genealogy of The Cilley Family; The Gamble Family; and The Mount Desert Widow. He was elected a member of the Maine Historical Society and a corresponding member of the New Hampshire Historical Society. He died in Alameda, California with his daughter Grace with whom he went to live in his old age. He died there 6 April 1920, and was buried in Thomaston 14 April 1920.

A plaque honoring General Jonathan Prince Cilley has been hung on Rockland's Wall of Fame located at the town hall.