Rotational atherectomy (RA) can facilitate smooth stent delivery and stent expansion through lesion modification for a calcified coronary lesion. Several studies reported that sirolimus-eluting stent (SES) implantation following RA showed a lower rate of revascularization compared with bare-metal stents (BMS). However, there are limited data that compared the clinical outcomes between SES and paclitaxel-eluting stents (PES) after RA. We compared the long-term clinical outcomes of SES and PES following RA. Two hundred and thirty-three consecutive patients (SES n = 179, PES n = 54) who were treated with SES or PES following RA between 10th September 2004 and 13th April 2010 were investigated. Follow-up data for clinical outcomes were obtained in 91.4% of all subjects. The median follow-up period was 630 days (interquartile range, 300 to 1170 days) in the SES group, and 625 days (interquartile range, 285 to 900 days) in the PES group. Clinical outcomes including target lesion revascularization (TLR) (SES 4.9% versus PES 9.8%, P = 0.31), target vessel revascularization (TVR) (SES 6.8% versus PES 11.8%, P = 0.25), and major adverse cardiac events (MACE) (SES 14.8% versus PES 13.7%, P = 0.8) were not statistically different between the groups. The unadjusted cumulative event rates estimated by the Kaplan-Meier method and the log-rank test showed no significant differences between the two groups for time to event for TLR, cardiovascular death, all-cause death, or MACE. In conclusion, there was no significant difference in the long-term clinical outcomes between SES and PES following RA.