Hudner was promoted to captain in 1965, taking command of Training Squadron 24 at Naval Air Station Chase Field in Bee County, Texas, which he commanded in 1965 and 1966. In 1966 he was assigned to USS Kitty Hawk, first as a navigator, then as the ship's executive officer. Kitty Hawk deployed off the shore of South Vietnam in 1966 and 1967, launching missions in support of the Vietnam War, and he served on the ship during this tour but saw no combat and flew none of the missions himself.