At the start of the Civil War in 1861, Hooker requested a commission, but his first application was rejected, possibly because of the lingering resentment harbored by Winfield Scott, general-in-chief of the Army.
Ved borgerkrigens start bad Hooker om at få en kommando, men hans første ansøgning blev afslået, formentlig på grund af fortsat harme hos general Winfield Scott, hærens øverstkommenderende.