Yakushima is a small, mountainous island off southern Kyushu, Japan. Its proximity to active volcanos and subduction zones leaves Yakushima vulnerable to large megathrust earthquakes and tsunamis, in addition to powerful typhoons and storm surges. These hazardous events deposit beach boulders: large rocks moved above sea-level by powerful waves. By radiocarbon dating the fossilized coral within these boulders, one can derive age estimates of the hazard events. Reliably estimating the magnitude and timing of geological events in the historical record is vital for future hazard prediction and mitigation. In this study, we estimated the deposition age of ten boulders on the north coast of Yakushima to infer potential paleo tsunamis and storm surges. We found that large wave events have occurred frequently throughout the Holocene. Based on the boulders’ ages, we identified four potential deposition events at 1986–2692 cal yr BP, 3522–4075 cal yr BP, 4773–5232 cal yr BP, and 6187–6638 cal yr BP. These deposits are likely a result of storm surges, or tsunamis from nearby volcanic activity or subduction earthquakes. Another set of boulders dated to 5125–5738 cal yr BP were likely exposed due to a decline in sea-level following the Holocene high sea-level stand. Further modelling could determine the wave height necessary to move the boulders and distinguish between storm and tsunami deposits. This is especially pertinent given the high frequency of coastal geohazards, and the likelihood of similar hazards impacting southeast Japan in the future.