The basin‐wide response of the Indo‐Pacific Ocean to atmospheric forcing associated with the Intraseasonal Oscillation (ISO) is examined using an ocean general circulation model forced by canonical ISO conditions constructed from observations. The results show that the imposed ISO forcing induces ocean variability that both is local to the region of intense convective activity and has considerable variability outside this region. In the areas most strongly and directly affected by ISO forcing, mixed layer depth variations were found to be considerable and tended to contribute positively to the magnitude of the sea surface temperature (SST) variations. In addition, there are a number of places where variations in entrainment and three‐dimensional ocean advection make nontrivial contributions to the mixed layer heat budget. Large values of entrainment variability in the Bay of Bengal signify one noteworthy difference between this and the austral summer case, which showed no large‐scale ocean regions exhibiting significant entrainment variability. The ISO‐related intraseasonal variability that occurred in regions remote from the ISO forcing include SST variability in the equatorial eastern Pacific that was generally analogous to the eastern Pacific variability associated with the austral summer case. ISO wind stress forcing induces remotely forced sea level variations, via Kelvin waves, on the equator and the eastern sides of the Indian and Pacific basins. In the case of the Indian Ocean these variations are on the order of 5–10 cm and travel in a matter of weeks from the central basin well into the Bay of Bengal as well as southward along Java and into the Indonesian seas. In conjunction with these sea level variations are variations in basin‐wide transports. Specifically, variations in the Indonesian Throughflow (ITF) brought about by ISO forcing are of the same order of magnitude as the seasonal cycle of ITF transport (∼1 PW; 10 Sv). In contrast, the variations associated with the climatological cross‐equatorial flow in the Indian Ocean basin are considerably larger (∼±2 PW; 20 Sv) than those associated with ISO forcing (∼±0.2 PW; 2 Sv). The results also showed that the imposed ISO forcing and associated ocean response exhibit a low‐frequency rectification, namely a mean SST warming (∼0.1°C) and MLD shoaling (∼7 m) over much of the northern Indian and northwestern tropical Pacific Oceans. The implications and caveats associated with the above results, the caveats associated with the model and forcing framework, and the areas necessitating further study are discussed.