Background: Thin-strut biodegradable polymer sirolimus-eluting stents (BP-SES) have been shown to reduce target lesion failure (TLF) at one-year follow-up compared with durable polymer everolimus-eluting stents (DP-EES) among patients with acute coronary syndrome (ACS). The long-term clinical benefits of thin-strut BP-SES over DP-EES in ACS patients after complete degradation of the polymer coating remain uncertain. Methods: We performed a post-hoc subgroup analysis of ACS patients included into the BIOSCIENCE randomized trial (NCT01443104). The primary endpoint was target lesion failure (TLF), a composite of cardiac death, target-vessel myocardial infarction or clinically indicated target lesion revascularization, at 5 years. Results: Among 2119 patients enrolled between March 2012 and May 2013, 1131 (53%) presented with ACS. The 5-year cumulative incidence of TLF was significantly lower in patients with ACS compared to chronic coronary syndrome [16.5% vs. 22.9%; rate ratio (RR), 0.69; 95% confidence interval (CI), 0.57-0.85; p < 0.001]. At 5 years, TLF occurred similarly in ACS patients treated with BP-SES and DP-EES (16.9% vs. 16.0%; RR, 1.04; 95% CI, 0.78-1.41; p = 0.78). The individual components of the primary endpoint did not differ between ACS patients treated with BP-SES or DP-EES at 5 years. Overall, there was no interaction between clinical presentation and treatment effect. Conclusions: In a subgroup analysis of the BIOSCIENCE trial, we found no difference in long-term outcomes between ACS patients treated with BP-SES or DP-EES at 5 years.