A linkage between climate change in the Atlantic and the Pacific oceans during the 1990s is investigated using three versions of the coupled climate model MIROC and CMIP5 multi-model ensemble. From the early 1990s to the early 2000s, the observed sea surface temperature (SST) shows warming in the North Atlantic and a La Niña-like pattern in the Pacific. Associated with the SST pattern, the observations indicate a strengthened Walker circulation in the tropical Pacific and enhanced precipitation in the tropical Atlantic. These SST and precipitation patterns are simulated well by hindcast experiments with external forcing and an initialized ocean anomaly state but are poorly simulated by uninitialized simulation with external forcing only. In particular, the observed La Niña-like SST pattern becomes prominent in ensemble members with large amplitudes of Atlantic Multidecadal Oscillation (AMO) index during 1996–1998. Our results suggest that ocean initialization in both the Pacific and the Atlantic plays an important role in predicting the Pacific stepwise climate change during the 1990s, which contributes to the accurate estimation of global temperature change in the coming decade. Forecasting typhoon frequency or marine fisheries production in the coming decade may be possible by improving the predictive skill of stepwise climate change.