Glacio-eustasy has been shown to be a primary control on sedimentation in the open ocean and along passive continental margins, but its importance in clastic-dominated deep-marine sequences at active plate margins remains poorly understood. In order to test the relative importance of glacio-eustasy at tectonically active plate margins during times of substantial polar ice, a high-resolution δ1SO and δ13C record from planktonic foraminifera (Globorotalia inflata) was undertaken from the Plio-Pleistocene (c. 1180–600 ka) Kazusa Group, a forearc basin fill, onland SE Japan. This was combined with a high-resolution study of the magnetic susceptibility, total organic carbon, and %CaCO3 in order to evaluate the response to any glacio-eustatic changes in continental-margin sedimentary processes. The sections reveal globally recognized glacial-interglacial cycles, with sandy intervals correlating with inferred glacials, suggesting that relative sea-level changes during glacial-interglacial cycles exerted the primary control on sediment accumulation in the deep-marine forearc basin. Cross-spectral analysis of δ18O and δ 13C data from the inter-turbidite hemipelagic and pelagic mudstones reveals Milankovitch control both at precession and eccentricity modes, with a shift in their relative importance at about 900 ka. The results of this study have important implications for stratigraphers and sedimentologists because they show that at times when there is substantial polar ice: (1) the main control on sediment accumulation at active plate margins is glacio-eustatic, and (2) support the sequence stratigraphic paradigm developed from passive continental margins that global sea-level changes exert a primary control on siliciclastic deposition.