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Abstract Ocean surface rain layers (RLs) form when relatively colder, fresher, less dense rain water stably stratifies the upper ocean. RLs cool sea surface temperature (SST) by confining surface evaporative cooling to a thin near‐surface layer, and generate sharp SST gradients between the cool RL and the surrounding ocean. In this study, ocean‐atmosphere coupled simulations of the November 2011 Madden‐Julian Oscillation (MJO) event are conducted with and without RLs to evaluate two pathways for RLs to influence the atmosphere. The first, termed the “SST gradient effect,” arises from the hydrostatic adjustment of the boundary layer to RL‐enhanced SST gradients. The second, termed the “SST effect,” arises from RL‐induced SST reductions impeding the development of deep atmospheric convection. RLs are found to sharpen SST gradients throughout the MJO suppressed and suppressed‐to‐enhanced convection transition phases, but their effect on convection is only detected during the MJO suppressed phase when RL‐induced SST gradients enhance low‐level convergence/divergence and broaden the atmospheric vertical velocity probability distribution below 5 km. The SST effect is more evident than the SST gradient effect during the MJO transition phase, as RLs reduce domain average SST by 0.03 K and narrow vertical velocity distribution, thus delaying onset of deep convection. A delayed SST effect is also identified, wherein frequent RLs during the MJO transition phase isolate accumulated subsurface ocean heat from the atmosphere. The arrival of strong winds at the onset of the MJO active phase erodes RLs and releases subsurface ocean heat to the atmosphere, supporting the development of deep convection.