Ellis saw his first combat action at the First Battle of Bull Run. He was then asked by Charles H. Van Wyck to help train the 56th New York Volunteer Infantry, a three-years' volunteer regiment. On September 5, 1862, Ellis became the first colonel of the newly raised 124th New York Infantry.
Ellis's military career began when he saw action at the First Battle of Bull Run. He was subsequently asked to lead a volunteer regiment from New York, which he became the first commander of on September 5, 1862.