Stone fought in the Mexican–American War, served as a Union Army general during the American Civil War, and later served as a general in the Egyptian Army. He is also noted for his role in constructing the base of the Statue of Liberty.
Stone graduated seventh out of 41 cadets from the United States Military Academy at West Point in 1845, and was brevetted a second lieutenant of ordnance. He was promoted to second lieutenant on March 3, 1847. Stone served with Maj. Gen. Winfield Scott's army in the Mexican-American War, and was brevetted to first lieutenant for the Battle of Molino del Rey on September 8 and to captain for the Battle of Chapultepec on September 13. After Mexico he was promoted to first lieutenant on February 26, 1853.
Stone then traveled through Europe for two years, learning European armies' ordnance techniques. He spent five years as Chief of Ordnance of the Pacific Department, locating sites for forts and arsenals, and establishing the Benicia Arsenal in California. Stone resigned his commission on November 17, 1857,, and after a brief but unsuccessful banking career was employed by the Mexican government as a surveyor, leading a scientific expedition in the Mexican state of Sonora.
Stone was appointed Colonel of the 14th U.S. Infantry Regiment on May 14, and then a brigadier general of volunteers in August, to rank from May 17. He commanded a brigade in Maj. Gen. Robert Patterson's Army of the Shenandoah during the First Bull Run campaign and afterward commanded a division (called the Corps of Observation) guarding the fords on the upper Potomac River.
Without assignment until May 1863, Stone was ordered to the Department of the Gulf, serving as a member of the surrender commission at Port Hudson and in the Red River Campaign as Maj. Gen. Nathaniel P. Banks's chief of staff. However, on April 4, 1864, Stanton ordered Stone mustered out of his volunteer commission as a brigadier general and he reverted to his rank of colonel within the regular army. He served briefly as a brigade commander in the Army of the Potomac during the Siege of Petersburg, but finally resigned from the Army on September 13, 1864, before the end of the war.
Stone later returned to the United States, where he served as the Chief Engineer for the construction of the Statue of Liberty's pedestal and concrete foundation. He fell ill after the dedication ceremony and died in New York City. He is buried in West Point National Cemetery.
Stone was married twice, first in 1853 to Maria Clary with whom one daughter was born. Maria died in Washington, D.C., shortly after Stone's release from Fort Hamilton. While serving in New Orleans during 1863, Stone fell in love with and married a distant relation, Jeanne Stone. Charles and Jeanne Stone had two daughters and a son, John Stone Stone, who later became a pioneer in the field of wireless telegraphy.