Jones attends grammar school in Dublin for three years until emigrating with his family to the United States in 1840. They settle on a farm in Cattaraugus County, New York where Jones spends most of his childhood. Because of his poor background, he receives only a limited education at the Union School in Ellicottville. In 1850, the 20-year-old Jones becomes involved in journalism and travels as a correspondent throughout the Western States for a leading New York journal. He later becomes the local editor for the Buffalo Republic and one of the editors of the Buffalo Sentinel.
Eventually, Jones decides to pursue a career in law and later studies under the firm of Addison Rice. He is admitted to the bar in 1856 and afterwards practices law with Addison in Ellicottville as a full partner. By 1860, he has established himself as one of the most prominent lawyers in western New York. A lifelong Democrat, he becomes disillusioned by the party’s support of Southern succession from the Union and, in May 1861, decides to join the military in defense of the United States.
Upon the outbreak of the American Civil War, Jones readily joins the Union Army. On July 7, 1861, he enlisted with the 37th New York Volunteers, popularly known as the “Irish Rifles”, under Colonel John H. McCunn. Jones has a successful career serving in the Union Army, being involved in thirty major battles and countless skirmishes, and reaching the rank of brigadier general. He remains at that rank for the rest of the war and resigns on June 17, 1865. He is one of ten Irish Americans to become brigade commanders and one of four Irish-born officers to become a divisional commander.
After his resignation, Jones resumes his law practice in Ellicottville and in November 1865 is elected on the Republican ticket as Clerk of the New York Court of Appeals. On August 13, 1868, Jones is appointed by Gov. Reuben E. Fenton as Register of New York City to fill the vacancy resulting from the death of Charles G. Halpine. On April 1, 1869, Jones is appointed by President Ulysses S. Grant as Postmaster of New York City. From 1875 to 1877, Jones is again Register of New York City, elected in November 1874 on the Republican ticket. Afterwards he resumes his private practice.
In 1878, Jones is involved in the Alexander T. Stewart bodysnatching case when he is contacted by the kidnappers to act as an intermediary between themselves and the Stewart estate. When negotiations stall between the Stewart family’s lawyer Henry Hilton, he assists Stewart’s widow in negotiating for the return of her husband’s body.
Jones suffers serious medical problems in his old age, specifically deafness and chronic diarrhea, which his physician blames on his exposure to artillery fire and his time in the swamps along the Chickahominy River during his military service. He also suffered from constant pain in his right sciatic nerve, attributed to his old war wound suffered at Chancellorsville, as well as his wound in the gluteal region.
In early July 1900, Jones begins suffering from severe gastroenteritis. His condition does not respond to therapeutic treatments as he loses control of his bowels and is unable to keep down solid food, living on scalded milk and brandy. On July 18, 1900, Jones dies from cardiac failure, indirectly caused by his gastroenteritis, at his home in Port Richmond, New York. His funeral is held at St. Mary’s Church two days later and he is buried in St. Peter’s Cemetery.