Eocene to Lower Miocene coal‐bearing formations in northern and western Kyushu, northern Ryukyu arc, are folded, and the horizontal compression has been attributed to the opening of the Japan Sea or to the significant movement along the Median Tectonic Line and its southwestern extension. However, the timing and implication of the folding are not well understood. To deal with these issues, we studied the Amakusa region where the folded Eocene strata with a total thickness of a few kilometers. Paleomagnetic directions of Middle Miocene intrusions and of Late Miocene lavas were measured in this study to apply the fold test to judge the relative timing of the folding and magmatism. As a result, the concentration of the directions was improved by the tilt‐correction, indicating the folding younger than the magmatism. Our detailed geological mapping revealed that the folding is older than a horizontally‐lying basaltic lava which yielded a K–Ar age of 6.8 Ma, because folded Eocene formations were truncated and unconformably blanketed by the lava. In addition, we found that some of the normal faults trending perpendicular to the folds were reactivated as transfer faults after the normal faulting which also postdated the magmatism. This reactivation is concordant with the above‐mentioned relative timing. Synthesizing geological data from surrounding regions, we conclude that the folding was probably contemporaneous with the Taiwan‐Shinji fold belt which grew in the Ryukyu and southwest Japan backarcs. Since the simultaneous compression affected not only these regions but also northeast Japan, the compression possibly resulted from the resumed subduction of the Philippine Sea Plate in the Serravallian–Tortonian time.