© 2019, The Author(s). The 2011 Tohoku-oki earthquake generated a large tsunami that caused catastrophic damage along the Pacific coast of Japan. The major portion of the damage along the Pacific coast of Tohoku in Japan was mainly caused by the first few cycles of tsunami waves. However, the largest phase of the tsunami arriving surprisingly late in Hakodate in Hokkaido, Japan; that is, approximately 9 h after the origin time of the earthquake. It is important to understand the generation mechanism of this large later phase. The tsunami was numerically computed by solving both linear shallow water equations and non-linear shallow water equations with moving boundary conditions throughout the computational area. The later tsunami phases observed on southern Hokkaido can be much better explained by tsunami waveforms computed by solving the non-linear equations than by those computed by solving the linear equations. This suggests that the later tsunami waves arrived at the Hokkaido coast after propagating along the Pacific coast of the Tohoku region with repeated inundations far inland or reflecting from the coast of Tohoku after the inundation. The spectral analysis of the observed waveform at Hakodate tide gauge shows that the later tsunami that arrived between 7.5 and 9.5 h after the earthquake mainly contains a period of 45–50 min. The normal modes of Hakodate Bay were also computed to obtain the eigen periods, eigenfunctions, and spatial distribution of water heights. The computed tsunami height distributions near Hakodate and the fundamental mode of Hakodate Bay indicate that the large later phases are mainly caused by the resonance of the bay, which has a period of approximately 50 min. The results also indicate that the tsunami wave heights near the Hakodate port area, the most populated area in Hakodate, are the largest in the bay because of the resonance of the fundamental mode of the bay. The results of this study suggest that large future tsunamis might excite the fundamental mode of Hakodate Bay and cause large later phases near the Hakodate port. [Figure not available: see fulltext.].