The son of General Thomas Newton, John was a convert to Catholicism. He graduated from the United States Military Academy in 1842, was commissioned a major in 1861, distinguished himself in the Civil War, and in 1865 was brevetted major-general of volunteers, brigadier-general and major-general of regulars. He was commissioned lieutenant-colonel of engineers in the regular service in 1865, superintending the work on the improvement of the Hudson River between Troy and New York on the channel between New Jersey and Staten Island, the harbors on Lake Champlain, and removed the dangerous rocks in Hell Gate, the water-way between the East River and Long Island Sound. Received the Laetare Medal in 1886. He was made commissioner of public works of New York in 1886, a post he resigned to become president of the Panama Railroad Company in 1888.