At the commencement of the civil war, he and his son, Wesley F. Miller, enrolled themselves as private soldiers in the First Minnesota regiment. On April 29, 1861, he was mustered into the service as lieutenant colonel of the First Minnesota. He was commissioned colonel of the Seventh regiment of Minnesota volunteers Sept. 26, 1862, and was made brigadier general of volunteers by the president Oct. 26, 1863. He took part in many of the important battles of the civil war and played an important part in the Sioux war, serving under General Sibley. He was in charge of the forces at Mankato on Dec. 26, 1862, which executed the thirty-eight Indians.
Stephen Miller was elected governor of Minnesota on the Republican ticket in November, 1863, and served until January 8, 1866. From 1871 until 1878, Governor Miller was employed as a field agent for the St. Paul & Sioux City Railroad company, and lived in Windom, MN. In 1878, he moved to Worthington, MN, which was his home until he died on August 18, 1881. He is buried in the Worthington Cemetery.
The Stephen Miller Post #139 was organized on May 21, 1885. That evening, 22 Civil War veterans were mustered in. In 1920, there were still four surviving members. The post disbanded in 1923, when the members numbered only two: James L. Hendron and James Newton Baker, who both then joined Pipestone's post.