While the Madden–Julian Oscillation (MJO) has been shown to affect tropical cyclones (TCs) worldwide through its modulation of large-scale circulation in the atmosphere, little or no role for the ocean has been identified to date in this influence of MJO on TCs. Using observations and numerical model simulations, we demonstrate that MJO events substantially impact TCs over the Maritime Continent (MC) region through an oceanic pathway. While propagating across the MC region, MJO events cause significant sea surface cooling with an area-averaged value of about 0.35 ± 0.12 °C. Hence, TCs over the MC region immediately following the passage of MJO events encounter considerably cooler sea surface temperatures. Consequently, the enthalpy fluxes under the storms are reduced and the intensification rates decrease by more than 50% on average. These results highlight an important role played by the ocean in facilitating MJO-induced sub-seasonal variability in TC activity over the MC region.