Returning to West Point in 1850 as the Assistant Professor of Geography, History and Ethics he was promoted to first lieutenant on June 10, 1850.

During the Confederate Heartland Offensive, Maj. Gen. William "Bull" Nelson was wounded in the battle of Richmond and his Army of Kentucky severely mauled.

Department commander Horatio G. Wright needed to select a replacement for the wounded Nelson and the two ranking officers, Generals Charles Cruft and James S. Jackson, refused the promotion.

[4] Several days later, on September 9, President Abraham Lincoln promoted Gilbert to brigadier general of U.S.

[6] Proudly wearing two stars in his shoulders, Gilbert was temporarily placed in command of the corps-sized Army of Kentucky in the absence of Nelson.

Some officers in the Army, including Buell's Chief of Staff James B. Fry, were surprised to find out Gilbert had not officially been promoted to major general.

In July 1863 he was assigned to the East on administrative duty, serving as Assistant Provost Marshal General and Chief Mustering Officer in Philadelphia, Pennsylvania and later Hartford, Connecticut, for the remainder of the war.