Kiernan insisted on joining the fighting ranks, and in that capacity was seemingly appointed a Major in the 6th Missouri. In May 1863 at Port Gibson, Missouri, he was wounded in the left lung and left on the field for dead. Recovered and imprisoned, he effected an escape back to Union forces and resigned his commission. On 1 August 1863 he was commissioned a Brigadier General of Volunteers by President Abraham Lincoln; commanding a post at Miliken's Bend on the Mississippi. However ill-health as a result of his battlefield wounds forced him to resign on 3 February 1864.