When the New York State Agricultural College (later merged into Cornell University) was founded in Ovid, New York, Kimball became Professor of Chemistry and Economic Geology. With the outbreak of the American Civil War in 1861, the college's president, Maj. M. R. Patrick was appointed Brigadier-General of Volunteers; Kimball became Brig. Gen. Patrick's Chief of Staff, with the rank of Captain. He saw field service under Maj. Gen. Irvin McDowell, and was present at the Second Battle of Bull Run (August 28–30, 1862); the Battle of Chantilly (September 1, 1862); the Battle of South Mountain (September 14, 1862); the Battle of Antietam (September 17, 1862); the Battle of Fredericksburg (December 11–15, 1862); the Battle of Chancellorsville (April 30-May 6, 1863); and the Battle of Gettysburg (July 1–3, 1863). Brig. Gen. Patrick was then appointed Provost Marshal of the Army of the Potomac, and Capt. Kimball accompanied him there, serving on the General Staff under Generals George B. McClellan, Ambrose Burnside, Joseph Hooker, and George Meade successively.