A very large acceleration of 1.6 g was observed on the first floor of the Meiwa Elementary School, Hokkaido, during the largest aftershock of the 1993 Hokkaido-Nansei-Oki earthquake. In order to investigate the cause of this very large acceleration, this paper described the building three-dimensionally as an assembly of nonlinear elements because its plan was not a simple rectangle, and then the base-rock motions were estimated at a depth of 8.6 m after evaluating the soil-structure interaction. The resultant base-rock motions made it clear that the large acceleration of 1.6 g was ascribed mainly to the amplification factor of up to 30 at about 4 Hz from the base rock to the first floor of the building.