Seepage of methane-rich fluids is common in subduction zones throughout Earth's history. However, the causes and hydrogeological regimes of methane seepage in the geological past are commonly elusive. To provide insights into the hydrogeological regime and structural evolution of the Cretaceous subduction zone of Hokkaido, Japan, this study investigates the timing of discharge and migration pathways of fluids emitted at five ancient methane seeps using U–Pb dating and coupled Sr, Nd, C, and O isotope analyses of the authigenic seep carbonates. The carbonates were collected from forearc-basin sediments of the Yezo Group, which are underlain by a mafic igneous basement (lower Sorachi ophiolite) detached from the subducting plate. The subduction zone is known to have experienced intermittent accretionary and non-accretionary stages, and the U–Pb dates determined for seep carbonates document two fluid discharge events, ∼100 and ∼80 Ma, falling within the accretionary periods. The 87Sr/86Sr ratios (0.70682–0.70781) and εNd values (−5.9 to −0.1) of the carbonates show significant variability, indicating the seeping fluids experienced interactions with the mafic rocks of the lower Sorachi ophiolite and with siliciclastic sediments of the Yezo Group. The δ13C values of the carbonates, as low as −49‰, suggest a primarily microbial origin of the seeping methane, which makes methane migration from the underplating materials at high temperatures (>100 °C) unlikely. These results demonstrate that the episodic expulsion of the methane-rich fluids, originating from within the forearc basin rather than from the underplating materials, occurred during the accretionary stages and played a major role in methane seepage in the Cretaceous subduction system.