The Median Tectonic Line (MTL) in Southwest Japan, a major east‐west trending arc‐parallel fault, has been defined as the boundary fault between the Cretaceous Sambagawa metamorphic rocks and the Ryoke granitic and metamorphic rocks, which are unconformably covered by the Upper Cretaceous Izumi Group. Based on the detailed fieldwork and microstructural studies of fault rocks, we reconstruct the kinematic history along the MTL during the Paleogene, which can be divided into the Ichinokawa and pre‐Tobe phases. While the Ichinokawa phase is defined by large‐scale, top‐to‐the‐north normal faulting, the pre‐Tobe phase is represented by large‐scale, high‐angle right‐stepping en échelon faults almost parallel to the MTL in the Upper Cretaceous Izumi Group. We found that left‐handed en échelon folds have developed along the right‐stepping faults, which contain 25–60 m wide cataclasite and fault gouge. Both map scale en échelon folds and microstructures (e.g., composite planar structures) in the fault rocks suggest that they were formed by sinistral‐reverse faulting with top‐to‐the‐SW kinematics. Furthermore, based on the new K‐Ar age dating of authigenic illite from the fault gouge along the MTL and right‐stepping faults, it can be concluded that the MTL was activated in two discrete stages at approximately 59 Ma (Ichinokawa phase) and 47–46 Ma (pre‐Tobe phase). Based on these results, we reappraise the kinematic framework of the MTL in the Paleogene, which can be interpreted as the record of the movements of the subducting oceanic plate relative to the continental plate. Key Points The kinematics of the Median Tectonic Line (MTL), a major arc‐parallel fault in SW Japan, are investigated and dated by the K‐Ar method In the Paleogene, large‐scale normal faulting at approximately 59 Ma is followed by sinistral‐reverse faulting at 47‐46 Ma along the MTL These kinematic histories of the MTL are well‐correlated with the reconstructed plate motion in the Pacific region in geological time