On June 14, 1898, Paddock and the 6th Cavalry departed Florida for Cuba and the Spanish–American War. There he was recognized for gallantry during the Battle of San Juan Hill in the Santiago Campaign. While in Cuba, Paddock contracted malaria, and was on sick leave by September 1898. Despite a favorable diagnosis, Paddock was on frequent medical leave or under medical care throughout 1899 while stationed at Fort Leavenworth.