With the outbreak of the American Civil War in 1861, Emmons enlisted in the Union Army, serving in Company K of the 1st Michigan Cavalry. Emmons, who began as a private and rose all the way to captain, was also part of the Michigan Brigade, which was under the command of Brigadier General George Armstrong Custer. This brigade, a collection of various Michigan cavalry regiments, fought in every major campaign of the war from the Battle of Gettysburg in July 1863 to the Battle of Appomattox Courthouse in April 1865.