Abstract Neotectonic crustal deformation in central Japan is described quantitatively on the basis of paleomagnetic measurements and numerical modeling. The welded part of the earliest Quaternary Nyukawa Pyroclastic Flow Deposit (NPFD) preserves stable remanent magnetization. Detailed paleo-/rock magnetic experiments reveal that remanence of the NPFD near the Takayama Basin resides in unimodal titanomagnetite and comprises a component of thermoremanent magnetization (TRM) and three components of thermoviscous remanent magnetization (TVRM). Scatter in the untilted declinations of the syn-depositional TRM component represents differential rotation about vertical axes related to Quaternary activity of three faults (Enako, Makigahora and Harayama) associated with the Takayama Basin. The normal and reversed TVRM components, probably acquired by warm water circulation near the active faults during the Jaramillo Subchron, record a complicated rotational sequence since ca. 1 Ma. Dislocation modeling successfully simulates the spatial distribution of rotation and the uplift/subsidence pattern around the Takayama Basin assuming strike–slip motion on the Enako and Makigahora Faults along the basin margin and vertical displacements on the Harayama Fault within the basin. Temporal changes in rotational motions recorded in the TVRMs of near-fault sites can be modeled by considering transition of active segments of the three faults, which is geologically constrained.