The large-scale response of the Indo-Pacific Ocean to atmospheric forcing associated with the Madden-Julian Oscillation (MJO) is examined using an ocean general circulation model forced by canonical MJO conditions constructed from observations. The results show that for a number of equatorial areas, ocean advection processes can play an important role in determining the ocean response. In addition, mixed layer depth (MLD) variations are considerable and contribute to the sea surface temperature (SST) variability. SST variability also develops in the eastern equatorial Pacific via the propagation of ocean Kelvin waves. With regards to this variability the results suggest that advective processes, namely, meridional advection, play the most significant role. Sea level variability in the equatorial regions and eastern sides of the Indian and Pacific basins associated with the MJO is considerable. In conjunction with these sea level variations are also large variations in the Indonesian Throughflow. The results also show that the MJO forcing produces a low-frequency rectified signal consisting of a weak cooling in the equatorial western Pacific and Indian Ocean regions, a relatively larger warming around the maritime continent, a fair amount of MLD shallowing in most of the above regions, and a westward equatorial Pacific Ocean current anomaly. In addition, the heat flux variations associated with the MJO produce systematic variations in the east-west zonal gradient of Indian Ocean SST, which could influence the evolution of the Indian Ocean Zonal Mode. The implications and caveats associated with these results, the caveats associated with the model and forcing framework, and areas necessitating further study are discussed.