When the American Civil War began in 1861, Fesler sided with the Union. On August 30, 1861, he enlisted into the Union Army at Morgantown, Indiana. Fesler was made the Captain of Company G in the 27th Indiana Infantry Regiment. Fesler commanded his company at the Battle of First Winchester and at the Battle of Cedar Mountain. In 1862, Fesler's Regiment was assigned to the 12th Army Corps, in which it would remain throughout 1863. Fesler then commanded his company during the Battle of Antietam, near Sharpsburg, Maryland, on September 17, 1862. His regiment spent the winter of 1862 to 1863 camped at Stafford Courthouse, Virginia, and on February 13, 1863, Fesler was promoted Lieutenant Colonel of the 27th Indiana. In March 1863, the 12th Corps, of which the 27th Indiana was a part, was issued a star as its corps badge. On May 5, 1863, Fesler was wounded in action during the Battle of Chancellorsville, in Spotsylvania County, Virginia. He then temporarily commanded the 27th Indiana from July 2-3, 1863 during the Battle of Gettysburg when the colonel of the regiment was placed in command of its brigade. Fesler and his regiment then took part in quelling the New York City Draft Riots later that month.