Major sea surface warming of El Niño events has occurred frequently in the central Pacific in recent decades, which is distinct from the eastern Pacific warming of canonical El Niño events. Accordingly, the central-Pacific El Niño exerts distinct impacts on ecosystems, climate and hurricanes worldwide. The increased frequency of the new type of El Niño presents a challenge for El Niño research. Previous studies have proposed different indices to represent the two types of El Niño for better understanding, prediction and impact assessment. Here, we find that all popularly used indices for the central-Pacific El Niño show a dominant spectral peak at a decadal period with comparatively weak variance at interannual timescales. Our results suggest that decadal anomalies have an important contribution to the occurrence of the central-Pacific El Niño over past decades. Removing the decadal component leads to a significant reduction in the frequency of the central-Pacific El Niño in observations and in CMIP5 simulations of preindustrial, historical and future climate.