We present a new dataset of zircon U–Pb ages that document igneous activity in the SW Japan arc during middle Miocene time and discuss its relationship with the opening of the Japan Sea, Philippine Sea plate migration, and subduction of the young hot lithosphere of the Shikoku Basin. Precursory magmatism, characterized by dike and stock intrusions, started c. 15.6 Ma in both Kyushu and the Kii Peninsula. Most plutonism occurred between 15.5 and 13.5 Ma in an area 600 km long and 150 km wide. No along-arc trend was recognized in the U–Pb ages of igneous activity near the trench. Our data indicate that all near-trench middle Miocene igneous activity occurred immediately after the opening of the Japan Sea ceased, i.e. after 16 Ma, implying that melt extraction and the emplacement of granites in the near-trench region had some influence on the back-arc opening. Our data also imply that the trench–trench–trench-type triple junction between the Japan arc and the Izu–Bonin–Mariana arc must have reached the east side of the Kii Peninsula by 15.6 Ma. The wide distribution of contemporaneous magmatic activity along the arc requires a trench-parallel heat source, such as the subduction of a trench-parallel ridge or a young and highly segmented ridge–fracture zone system in addition to the hot wedge mantle condition related to the opening of Japan Sea.