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Pore pressure plays a key role in the generation of earthquakes in subduction zones. However, quantitative constraints for its determination are quite limited. Here, we estimate the subsurface pore pressure by analyzing the transient upwelling flow of drilling mud from borehole C0023A of the International Ocean Discovery Program (IODP) Expedition 370, in the Nankai Trough off Cape Muroto. This upward flow provided the first direct evidence of an overpressured aquifer in the underthrust sediments off Cape Muroto. To estimate the pre‐drilling pore pressure in the overpressured aquifer around a depth of 950–1,050 m below sea floor, we examined the measured porosities of core samples retrieved from nearby IODP wells; we then proceeded to explain the observed time evolution of the flow rate of the upwelling flow by modeling various sized aquifers through solving a radial diffusion equation. It was observed that for a permeability of 10−13 m2, the aquifer possessed an initial excess pore pressure of ∼5–10 MPa above the hydrostatic pressure, with a lateral dimension of several hundred meters and thickness of several tens of meters. The overpressure estimates from the porosity‐depth profile at Site C0023 differ from those at other drill sites in the region, suggesting the possible existence of multiple overpressured aquifers with a patchy distribution in the underthrust sediments of the Nankai Trough. As pore pressure is relevant in maintaining fault stability, the overpressured aquifers may be the source of slow earthquakes that have been observed around the drilling site. Plain Language Summary: Fault zones often act as barriers to fluid flow, which can lead to the formation of aquifers of pressurized fluid in the vicinity of the fault. It is well known that pore fluid pressure plays a key role in the generation of subduction zone earthquakes, however quantification of pore fluid pressures around subduction zone faults has, up to now, been limited. The International Ocean Discovery Program (IODP) Expedition 370 drilled the Nankai Trough subduction zone off Cape Muroto (Japan), where slow earthquakes have been observed. While drilling, we observed a transient upwelling flow of drilling mud from the borehole. This flow provided the first direct evidence of an overpressured aquifer around the plate boundary fault. To constrain the properties of the aquifer we modeled aquifers with varying properties, and found that the upwelling mud at the drill‐site was likely generated by an aquifer with a lateral extent of hundreds of meters and with pore pressures considerably higher than the typical (hydrostatic) pore fluid pressure expected at this depth. Our results suggest that slow earthquakes that occur near Cape Muroto may be caused by relatively small, scattered, highly‐pressurized subsurface aquifers like the one we intersected during Expedition 370. Key Points: A transient borehole mud flow confirmed the existence of an overpressured aquifer beneath the Nankai Trough décollement off Cape MurotoThe aquifer of ∼5–10 MPa excess pore pressure was distributed over a lateral extent of hundreds of metersThe overpressured aquifer may have been the cause of slow earthquakes observed near the drilling site [ABSTRACT FROM AUTHOR]