The Eastern Tropical Pacific (ETP) is one of the last regions where large aggregations of the critically endangered scalloped hammerhead shark (Sphyrna lewini) can still be observed. In this regard, we comparatively assessed the seasonality in S. lewini’s relative abundance within three marine protected areas (MPAs) of the ETP and explored its relationship with environmental factors such as temperature. Abundance standardization via generalized linear mixed models revealed that Galapagos Islands (Ecuador) held an overall higher relative abundance of S. lewini when compared to Cocos Island (Costa Rica) and Malpelo (Colombia). The greatest relative abundance was observed from June to October for Cocos, followed by Galapagos (January, September, and November) and Malpelo (December, February, and March). Our results suggest that S. lewini observed relative abundances are significantly affected by water temperature and years (all three sites), and by the seasons, dive schedule, visibility and moon phase (to a lesser extend). This research contributes to the understanding of the temporal and spatial fluctuations of S. lewini at oceanic aggregation sites to improve the decision-making tools for the integral regional climate-smart management of the species. We recommended future studies to model the effect of climate change in the abundance at aggregation sites and potential distribution shifts across the ETP.