During the Russo-Japanese War, he commanded "Akitsushima" during the Battle of the Yellow Sea on August 10, 1904. Promoted to captain in January 1905 Yamaya then commanded the cruiser during the crucial Battle of Tsushima on May 26, 1905. In June, he was appointed chief-of-staff of the IJN 4th Fleet, and in December was chief-of-staff of the IJN 2nd Fleet.