A fully coupled general circulation model is used to investigate the hypothesis that during Pliocene times tectonic changes in the Indonesian seas modified the Indo-Pacific heat transport and thus increased the zonal sea surface temperature gradient in the equatorial Pacific to its large, current magnitude. We find that widening the Indonesian seaway by moving the northern tip of New Guinea south of the equator leads to an increased inflow of South Pacific waters into the Indian Ocean, but because of potential vorticity constraints on cross-equatorial flow it also leads to reductions in both the inflow of North Pacific waters and the total Indonesian throughflow transport. The reduced throughflow is matched by increased eastward transport of warm and fresh North Pacific surface waters along the equator to the central equatorial Pacific. As a result, the Intertropical Convergence Zone lies closer to the equator and the western Pacific Warm Pool expands farther east than for present-day conditions. This reduces the delayed oscillator component of El Niño–Southern Oscillation (ENSO) and enhances the role of stochastic perturbations. Thus, with a more open Indonesian seaway, ENSO becomes weaker and more irregular.