Following the war, Stephenson returned to farming, eventually settling in Batavia, Jefferson County, Iowa. His wife gave birth to two sons, Milton on February 23, 1867, and Cyrus on March 3, 1872. For the rest of his life, Stephenson endured pain in his legs, and catalyptic fits from his head injury. He died on December 5, 1882, and his wife on April 15, 1922.