Ellis was involved with several local Rockford militia and cadet corps, including the one that organized by Col. Elmer Ellsworth, considered the first person killed in the American Civil War.
Ellsworth was a personal friend of future President Abraham Lincoln and founder of the Zouave Movement, popular during and before the Civil War.
Ellis volunteered for duty and was mustered in the 15th Regiment, 2nd Brigade, 4th Division of the Army of the Tennessee, in Freeport, Illinois.
On April 6, 1862, while in the Hornet's Nest, having been promoted to the rank of acting colonel, Ellis was struck multiple times by enemy fire, but he continued to direct his troops until a fatal bullet hit him.
After an elaborate funeral service, Ellis was buried in the family plot that he had bought only a few years earlier after the death of one of his daughters.
His weather worn gravestone is inscribed: "Ellis, Edward F.W., Lieutenant Colonel in the 15th Regiment Ill Vol, Killed in Action during the battle of Shiloh".
His uniform and sword were on display at the Winnebago County War Memorial building in downtown Rockford, across the street from the Main Library, for several years.