During the American Civil War, Crandall offered his services to help the sick and wounded from the Battle of Fair Oaks and the Battle of Fredericksburg. Seeing the conditions there led him to believe in the necessity of sending medical agents to help the wounded, and in the 1863 New York State Medical Society meeting he proposed a resolution to appoint a medical agent to Washington to look after New York's sick and wounded. The resolution was presented to and passed by the Governor and Legislature. When two of his brothers were wounded outside of Atlanta in 1864, he came to their assistance and worked in Nashville and Louisville hospitals for several weeks. He was appointed Surgeon of the 141st New York Volunteer Infantry, with the unanimous vote from the regiment's officers. As he was only just nominated for re-election to the State Assembly, he declined. In April 1865, Governor Fenton appointed him New York Military Agent at City Point, Virginia. He also served as Visiting Agent of Military Hospitals and worked in the various hospitals of the Department of the Potomac.