In 1900, Ōkubo was promoted to lieutenant general and chief-of-staff of the Inspectorate General of Military Training. In May 1902, he became commander of the IJA 6th Infantry Division. During the Russo-Japanese War, the IJA 6th Infantry Division was attached to the Japanese Second Army, but after the Battle of Shaho was transferred to the Japanese Fourth Army before the Battle of Mukden. After the war, he was awarded with the Order of the Rising Sun, 1st class and the Order of the Golden Kite, 2nd class. In July 1906, he was transferred to command the IJA 3rd Division and in September 1907 was elevated to the "kazoku" peerage with the title of "danshaku" (baron).