Previous studies have demonstrated that patients with small coronary artery lesions are at increased risk for late cardiac events after percutaneous coronary intervention. It remains uncertain whether second-generation drug-eluting stents have an advantage over first-generation drug-eluting stents in patients with small vessel lesions. Our aim was to compare in the 3-year clinical impact between second-generation everolimus-eluting stents (EES) and first-generation sirolimus-eluting stents (SES) in small vessel lesions. Four-hundred forty-four patients with small vessel lesions defined as reference diameter <2.5 mm were treated with EES (237 patients, 265 lesions) or SES (207 patients, 220 lesions) and completed 3-year follow-up. We compared the major adverse clinical events (MACE) between the two groups. EES had no significant impact on the MACE rate compared with SES (4.6 vs. 7.2%, p = 0.14). No significant differences were observed in the individual components of cardiac death (1.7 vs. 1.9%, p = 0.78), myocardial infarction (1.3 vs. 3.4%, p = 0.12), and ischemia-driven target lesion revascularization (2.3 vs. 4.6%, p = 0.13) in EES and SES, respectively. Stent thrombosis, however, was significantly less in the EES group than in the SES group (0.7 vs. 3.4%, HR: 0.53, 95% CI 0.38–0.88, p < 0.05). EES implantation did not significantly impact 3-year MACE rates compared to SES implantation in small vessel lesions. A significant reduction in the overall rate of stent thrombosis was observed in recipients of EES. While the SES group showed increasing rates of late and very late thrombosis, the EES group did not. EES offers a safe and effective treatment for small vessel lesions.