Substantial (∼2°C) basin averaged sea surface temperature (SST) cooling in the Banda Sea occurred in less than a 14-day period during the 2015 boreal winter Madden-Julian Oscillation (MJO). Such rapid and large cooling associated with the MJO has not been reported at least in the last two decades. Processes that control the substantial cooling during the 2015 MJO event are examined using high-resolution ocean reanalysis and one-dimensional (1-D) ocean model simulations. Previous studies suggest that MJO-induced SST variability in the Banda Sea is primarily controlled by surface heat flux. However, heat budget analysis of the model indicates that entrainment cooling produced by vertical mixing contributes more than surface heat flux for driving the basin-wide SST cooling during the 2015 event. Analysis of the ocean reanalysis further demonstrates that the prominent coastal upwelling around islands in the southern basin occurs near the end of the cooling period. The upwelled cold waters are advected by MJO-induced surface currents to a large area within the Banda Sea, which further maintains the basin-wide cold SST. These results are compared with another MJO-driven substantial cooling event during the boreal winter of 2007 in which the cooling is mostly driven by surface heat flux. Sensitivity experiments, in which initial temperature conditions for the two events are replaced by each other, demonstrate that the elevated thermocline associated with the 2015 strong El Niño is largely responsible for the intensified cooling generated by the vertical mixing with colder subsurface waters.