The superiority of everolimus-eluting stents (EES) over sirolimus-eluting stents (SES) for long-term clinical outcomes has not been yet firmly established. We conducted a systematic review and a meta-analysis of randomized controlled trials (RCTs) comparing EES directly with SES using the longest available follow-up data. We searched PubMed, the Cochrane database, and ClinicalTrials.gov for RCTs comparing outcomes between EES and SES and identified 13,434 randomly assigned patients from 14 RCTs. EES was associated with significantly lower risks than SES for definite stent thrombosis (ST), definite/probable ST, target-lesion revascularization (TLR), and major adverse cardiac events (MACE). The risks for all-cause death and myocardial infarction were similar between EES and SES. By the stratified analysis according to the timing after stent implantation, the favorable trend of EES relative to SES for ST, TLR, and MACE was consistently observed both within and beyond 1 year. The lower risk of EES relative to SES for MACE beyond 1 year was statistically significant (pooled odds ratio 0.77, 95% confidence interval 0.61 to 0.96, p = 0.02). In conclusion, the current meta-analysis of 14 RCTs directly comparing EES with SES suggested that EES provided improvement in both safety and efficacy; EES compared with SES was associated with significantly lower risk for definite ST, definite/probable ST, TLR, and MACE. The direction and magnitude of the effect beyond 1 year were comparable with those observed within 1 year.