Objective: Rotational atherectomy (RA) and newly developed second-generation drug-eluting stent (DES) support the strategy of longer stent deployment in comparison to short stent implantations in the past. However, studies analyzing the outcome of patients who received long stent implantation following RA are few in number. The present study compared the clinical outcomes of patients with the coronary arterial disease (CAD) who underwent RA with long stent implantation using first- and second-generation DES. Methods: A retrospective cohort study was performed at the single center from March 2003 to October 2019. Eighty-seven patients with CAD who underwent RA with ≥32 mm long stent implantation were enrolled in the study and divided into two groups according to the type of DES. As a primary endpoint, the cumulative 2-year incidence of major adverse cardiac events (MACE) including death, myocardial infarction (MI), target vessel revascularization, and stent thrombosis (ST) was compared by DES type. Adjusted interaction between the type of stent and clinical variables was estimated to determine the predictor variables of MACE. Results: The second-generation DES group was associated with a shorter procedure duration and more common usage of intravascular ultrasound in procedural characteristics. In the second-generation DES group, a trend toward a lower rate of MI and ST existed. All-cause mortality and cardiovascular mortality were not significantly different. When combined with MACE, we could identify a significant reduction in the second-generation DES group. Conclusion In comparison to the first-generation DES group, the second-generation DES group was associated with a lower rate of MACE for 2 years in patients who underwent RA with long stent implantation.