On May 10, 1898, while Chanler was in Tampa, he was offered a commission as captain and assistant adjutant general on the staff of Major General Joseph Wheeler, which he accepted. He served as acting ordnance officer, Cavalry Division, Fifth Army Corps, from May 23 to August 23, 1898. In June and July 1898 he fought in the Battle of Las Guasimas, the Battle of El Caney, at San Juan Hill, and in the Siege of Santiago de Cuba, for which he received a commendation from Major General Wheeler for "gallantry in battle". He was honorably discharged on October 3, 1898.