Among drug-eluting stents (DESs), the durable polymer everolimus-eluting stent (EES) and resolute zotarolimus-eluting stent (R-ZES) are widely used in clinical practice and have contributed to improve the outcomes of patients undergoing percutaneous coronary intervention (PCI). Few studies addressed their long-term comparative performance in patients with acute coronary syndrome (ACS). We aimed to investigate the 5 year comparative efficacy of EES and R-ZES in ACS. We queried ACTION-ACS, a large-scale database of ACS patients undergoing PCI. The treatment groups were analyzed using propensity score matching. The primary endpoint was a composite of mortality, myocardial infarction (MI), stroke, repeat PCI, and definite or probable stent thrombosis, which was addressed at the five-year follow-up. A total of 3497 matched patients were analyzed. Compared with R-ZES, a significant reduction in the primary endpoint at 5 years was observed in patients treated with EES (hazard ratio (HR) [95%CI] = 0.62 [0.54–0.71], p < 0.001). By landmark analysis, differences between the two devices emerged after the first year and were maintained thereafter. The individual endpoints of mortality (HR [95%CI] = 0.70 [0.58–0.84], p < 0.01), MI (HR [95%CI] = 0.55 [0.42–0.74], p < 0.001), and repeat PCI (HR [95%CI] = 0.65 [0.53–0.73], p < 0.001) were all significantly lower in the EES-treated patients. Stroke risk did not differ between EES and R-ZES. In ACS, a greater long-term clinical efficacy with EES vs. R-ZES was observed. This difference became significant after the first year of the ACS episode and persisted thereafter.