Chronic kidney disease (CKD) patients have worse adverse cardiovascular outcomes after percutaneous coronary intervention (PCI). Clinical outcomes comparing a limus-eluting stent (LES) to a paclitaxel-eluting stent (PES) in patients with CKD remain controversial. A systematic search was conducted using PubMed, EMBASE, and Cochrane Library. A pooled odds ratio (OR) and 95% confidence interval (CI) were used to calculate original data. We conducted heterogeneity, quality assessment, and publication bias analyses. A total of 17 trials involving 10,724 patients were included. No significant differences were found regarding target vessel revascularization, target lesion revascularization (TLR), stent thrombosis (ST), myocardial infarction (MI), all-cause mortality, and major adverse cardiac events (MACE) between first-generation LES implantation and PES implantation. Second-generation LES implantation was associated with lower rates of allcause mortality (OR, 0.56; 95% CI, 0.39-0.82; P = 0.003), MACE (OR, 0.61; 95% CI, 0.38-0.97; P = 0.04), and ST (OR, 0.45; 95% CI, 0.26-0.77; P = 0.004) compared with PES implantation. In all, the long-term allcause mortality rate was significantly lower after LES implantation than after PES implantation in patients with CKD (OR, 0.78; 95% CI, 0.66-0.93; P = 0.004). However, second-generation LES implantation resulted in a higher rate of TLR (OR, 2.23; 95% CI, 1.53-3.25; P < 0.001) than PES implantation in dialysis patients. In patients with CKD, first-generation LES and PES implantation had comparable mortality and morbidity. Second-generation LES implantation was superior to PES in reducing long-term mortality, MACE, and ST. However, PES may be more effective than LES in dialysis patients.