 He graduated from Kimball Union Academy in Meriden, New Hampshire in 1854, and attended Middlebury College for two years, until he was accepted as a cadet in the United States Military Academy on July 1, 1855.He graduated from West Point on July 1, 1860, standing 40th in a class of 41.

brevet 2nd Lieutenant Warner was assigned to the 10th U.S. Infantry, and, on February 28, 1861, was promoted to 2nd Lieutenant and transferred to the 8th U.S. Infantry.He was then promoted to 1st Lieutenant May 31, 1861, and assigned to Fort Wise, Colorado Territory.