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Since the late 1990s, land surface temperatures over Japan have increased during the summer and autumn, while global mean temperatures have not risen in this duration (i.e., the global warming hiatus). In contrast, winter and spring temperatures in Japan have decreased. To assess the impact of both global warming and global-scale decadal variability on this enhanced seasonal temperature contrast, we analyzed the outputs of 100 ensemble simulations of historical and counterfactual non-warming climate simulations conducted using a high-resolution atmospheric general circulation model (AGCM). Our simulations showed that atmospheric fields impacted by the La Nina-like conditions associated with Interdecadal Pacific Oscillation (IPO) have predominantly contributed to the seasonal temperature contrast over Japan. Compared with the impact of negative IPO, the influence of global warming on seasonal temperature contrasts in Japan was small. In addition, atmospheric variability has also had a large impact on temperatures in Japan over a decadal timescale. The results of this study suggest a future increase in heatwave risk during the summer and autumn when La Nina-like decadal phenomena and atmospheric perturbations coincide over a background of global warming.