McKean commanded at Jefferson City, Missouri, from December to March 1862. He was then given divisional command in the Army of the Tennessee on April 10. He fought in the Battle of Corinth in Mississippi on October 3–4, and then led his division until December 9. McKean then commanded numerous districts across Union-held departments throughout 1863, 1864, and until July 10, 1865. McKean was appointed to the rank of brevet major general on March 13 for his war service, and was mustered out of the volunteer service on August 24.