After the war, he was a superintendent of the United States Military Academy at West Point, New York.

He participated in the Battle of Antietam, in which he was wounded while acting commander of a brigade in the 1st Division, XII Corps.

Commissioned brigadier general of volunteers in November 1862, Ruger led his brigade of the XII Corps, Army of the Potomac, in the Battle of Chancellorsville, and commanded the division of Brig.

Ruger participated in Reconstruction as the military governor of Georgia and in the Freedmen's Bureau in Alabama in 1868.

In 1887 Ruger led the army's expedition into the Big Horn Mountains during the Crow War.