Abstract Background The true benefit of biodegradable polymer drug-eluting stent (BP-DES) over second-generation durable polymer drug-eluting stent (DP-DES) expected to be represented during late period of follow-up after percutaneous coronary intervention (PCI), but prior meta-analysis only evaluated short-term outcomes. Purpose We aimed to compare the long-term clinical outcomes after PCI with BP-DES versus second-generation DP-DES by a meta-analysis of randomized controlled trials. Methods Randomized controlled trials comparing BP-DES with second-generation DP-DES implantations were searched through PubMed, MEDLINE, EMBASE, and Cochrane databases. All-cause death, cardiac death, myocardial infarction (MI), target vessel revascularization (TVR), target lesion revascularization (TLR), and definite/probable stent thrombosis (ST) were compared between the groups. In addition, a landmark analysis with the landmark set at 1-year and a subgroup analysis based on stent characteristics were performed. Results Fifteen trials that included a total of 21311 randomized patients with at least 2 years follow-up were analyzed. At a median follow-up of 4.2 years, no significant differences in the risks of all-cause death (odds ratio [OR] 1.03, 95% confidence interval [CI] 0.94–1.14), cardiac death (OR 1.03, 95% CI 0.88–1.20), MI (OR 0.90, 95% CI 0.79–1.01), TVR (OR 0.96, 95% CI 0.82–1.12), TLR (OR 0.97, 95% CI 0.85–1.11), and definite/probable ST (OR 0.84, 95% CI 0.67–1.05) were found between the groups. In the 1-year landmark analysis, the rates of all-cause death (OR 1.04, 95% CI 0.93–1.17), cardiac death (OR 1.11, 95% CI 0.92–1.36), MI (OR 0.94, 95% CI 0.79–1.13), TVR (OR 0.95, 95% CI 0.73–1.23), TLR (OR 1.00, 95% CI 0.80–1.24), and definite/probable ST (OR 0.94, 95% CI 0.67–1.31) were similar between the groups. There were comparable rates of any study endpoints between the groups regardless of stent platform (stainless steel vs. alloy), the polymer degradation period (<6 months vs. >6 months) or the drug release duration (<6 months vs. >6 months) of BP-DES, or the DAPT duration (≥6 months vs. ≥12 months). However, the use of BP-DES with sirolimus eluting (OR 0.82, 95% CI 0.70–0.97), circumferential drug distribution (OR 0.79, 95% CI 0.65–0.96), thin strut (defined as <100μm; OR 0.83, 95% CI 0.70–0.97), or ultrathin strut (defined as <70μm; OR 0.78, 95% CI 0.64–0.94) were associated with lower rates of MI than did second-generation DP-DES. Moreover, BP-DES with circumferential drug distribution (OR 0.82, 95% CI 0.69–0.98) was predictive for reduced rates of TVR. Clinical outcomes Conclusions In this meta-analysis, long-term clinical outcomes were equivalent between BP-DES and second-generation DP-DES implantations. However, among BP-DESs, the improved risks of MI in those with sirolimus eluting, circumferential drug distribution, thin strut, or ultrathin strut and decreased rates of TVR in those with circumferential drug distribution were noted.