Fowler enlisted into the Union Army as the lieutenant colonel of the 14th Brooklyn on April 18, 1861, at the age of 35. On February 22, 1862, he was promoted to colonel of the regiment after Col. Alfred M. Wood was wounded at the First Battle of Manassas. Colonel Fowler was very active after the war with veterans' affairs and the 14th Brooklyn Association, helping veterans of the 14th Brooklyn with pension funds. He always attended the funerals of fallen 14th Brooklyn soldiers post-war. He was very highly respected in Brooklyn, New York and was a beloved hero of the Civil War.