After a year with the 2nd Wisconsin, he accepted a promotion to colonel of the 18th Wisconsin Infantry on April 29, 1862, succeeding Colonel James S. Alban—who was killed at the Battle of Shiloh. It was with some reluctance that Bouck accepted this assignment when it was offered by Governor Alexander Randall; he was strongly encouraged to do so by fellow Wisconsin officer Edward S. Bragg. Bouck led the 18th Wisconsin through two years of campaigning in the western theater of the war, serving in the Army of the Tennessee under Ulysses S. Grant and William Tecumseh Sherman. He resigned from service on January 4, 1864, and returned to Oshkosh.