In 1862, when a Sioux Indian uprising in Minnesota resulted in the deaths of hundreds of white settlers, Swisshelm was among those demanding the federal government punish the Indians. She toured major cities to raise public opinion about this issue and, while in Washington, D.C., met with Edwin M. Stanton, a friend from Pittsburgh and then Secretary of War. He offered her a clerkship in the government. She sold her Minnesota paper and continued to work as an army nurse during the Civil War in the Washington area until her job became available.