Objective Biocompatible polymer everolimus-eluting stents (EES) are associated with risk of stent thrombosis (ST); biodegradable polymer drugeluting stents (BP-DES) were designed to reduce these risks. However, the long-term benefits are not completely clear. Method We undertook a meta-analysis of randomized studies identified in systematic searches of MEDLINE, EMBASE, and the Cochrane Database. Primary outcome was the risk of ST. Results Twelve studies (11,692 patients) were included. Overall, compared with EES, BP-DES were associated with a broadly equivalent risk of definite and probable ST (OR, 0.91; 95% CI, 0.55 to 1.50; P = 0.71; I-2 = 0.0%), early ST (OR, 2.25; 95% CI, 0.78 to 6.47; P = 0.13; I-2 = 0.0%), late ST (OR, 3.57; 95% CI, 0.42 to 30.58; P = 0.25; I-2 = 0.0%) and very late ST (OR, 0.50; 95% CI, 0.05 to 5.52; P = 0.57). Meanwhile, there was no significant difference in all-cause mortality (OR, 1.07; 95% CI, 0.86 to 1.32; P = 0.54; I-2 = 0.0%), myocardial infarction (OR, 1.07; 95% CI, 0.88 to 1.30; P = 0.47; I-2 = 0.0%), target vessel revascularization (OR, 1.02; 95% CI, 0.86 to 1.21; P = 0.80; I-2 = 12.0%), and major adverse cardiac events (OR, 1.04; 95% CI, 0.93 to 1.16; P = 0.53; I-2 = 0.0%). Furthermore, angiographic data showed that in-stent and in-segment late luminal loss were similar between the two groups. Conclusions Compared with biocompatible polymer EES, biodegradable polymer stents appear to have equivalent clinical benefits.