Casey was then superintending engineer of coastal fortifications in Maine and involved in recruiting engineers for the duration of the war, until July 25, 1866. Casey became a major on October 2, 1863, and was made a brevet lieutenant colonel and colonel on March 13, 1865. During the war, he served with the North Atlantic Squadron during the First Expedition to Fort Fisher from December 8 to 29, 1864. The following year he was on the special board of engineers for work on Willet's Point from April 7 to June 20, and for work on Fort Preble, Fort Scammel, Fort Popham and Fort Knox on the Penobscot River from August 1865 to February 1866.