During the Russo-Japanese War, he received his first command, that of the cruiser . Following his promotion to captain in July 1904, he captained the cruiser , during the Battle of the Yellow Sea. During the war, Arima was the senior member of Tōgō's Combined Fleet staff. One of the architects of the plan to blockade the Russian Pacific Fleet in Port Arthur (which he had visited on his return to Japan from England the previous year), Arima was on two of the three missions, and personally commanded the failed Second Port Arthur blockade attempt, during which Commander Takeo Hirose was killed. Soon afterwards, he was reassigned from his field command to become commandant of the Takeshiki Guard District on Tsushima, where he remained for the rest of the war.