In this study, we simulated the transport of a large coralline boulder on southern Ishigaki Island of the Sakishima Islands, Japan, to evaluate local paleotsunami size in comparison to a well-known historical event (the 1771 Meiwa tsunami). According to the geological evidence, the boulder was deposited at 10 m elevation by two paleo-tsunami events. We assumed two types of fault models and eight dislocations for each fault. Then we investigated whether there are any combinations of the fault models that can satisfy the movement of the boulder from its presumed initial position to the present position by two tsunamis. Results show that several combinations of tsunami source models can satisfy the geological constraints. Our results revealed that at least one tsunami event during the prehistoric age was equivalent to or even larger than the 1771 tsunami in terms of the flow depth at the southeastern coast of the Ishigaki Island. Although the accuracy of this method depends strongly on the available geological evidence, we infer that the numerical modeling for boulder transport will have great value for evaluation of the local tsunami size, which is important for local tsunami risk assessment.