Exhumed faults are rough, often exhibiting topographic corrugations oriented in the direction of slip; such features are fundamental to mechanical processes that drive earthquakes and fault evolution. However, our understanding of corrugation genesis remains limited due to a lack of in situ observations at depth, especially at subducting plate boundaries. Here we present three-dimensional seismic reflection data of the Costa Rica subduction zone that image a shallow megathrust fault characterized by corrugated, and chaotic and weakly corrugated topographies. The corrugated surfaces extend from near the trench to several kilometres down-dip, exhibit high reflection amplitudes (consistent with high fluid content/pressure) and trend 11–18° oblique to subduction, suggesting 15 to 25 mm yr⁻¹ of trench-parallel slip partitioning across the plate boundary. The corrugations form along portions of the megathrust with greater cumulative slip and may act as fluid conduits. In contrast, weakly corrugated areas occur adjacent to active plate bending faults where the megathrust has migrated up-section, forming a nascent fault surface. The variations in megathrust roughness imaged here suggest that abandonment and then reestablishment of the megathrust up-section transiently increases fault roughness. Analogous corrugations may exist along significant portions of subduction megathrusts globally.