Ongoing excavations on Rebun Island have demonstrated the prehistoric use of obsidian persistently from the Middle Jomon (5400−4300 cal.YBP) to Okhotsk (1500−750 YBP) periods. Since obsidian does not occur naturally on Rebun Island, only the transportation of raw materials and/or finished tools over great distances accounts for their presence there. Previous research in northeast Asia has shown that movement of obsidian from various sources on Hokkaido played a vital role in the entire lithic industry since the Paleolithic. As cultures varied in Northern Japan from the Middle Jomon to the Okhotsk periods, the patterns of source exploitation are also believed to have changed. This expectation is tested by evaluating the sources of archaeological obsidian recovered from three archaeological sites on Rebun Island (Uedomari 3, Kafukai 1, and Hamanaka 2) through portable-XRF. This method provides new insights into the dynamics of resource procurement and distribution among Middle Jomon to Okhotsk hunter–gatherers on Rebun Island.