Drug-coated balloon (DCB) angioplasty has been shown to be a promising option for the treatment of coronary in-stent restenosis (ISR). We compared the clinical outcomes of patients with ISR who were treated with two commonly used paclitaxel-containing DCBs, the Pantera Lux (PL) and SeQuent Please (SP). A total of 491 patients with 507 ISR lesions [PL-DCB in 127 (26%) patients and SP-DCB in 364 (74%) patients] underwent DCB angioplasty for ISR lesions. The major adverse cardiac events (MACEs), including cardiac death, target lesion-related myocardial infarction, and target lesion revascularization, were assessed. There were no significant differences in each occurrence of MACE and cardiac death: 16 MACEs (61 per 1000 person-years) in the PL-DCB group and 55 (60 per 1000 person-years) MACEs in the SP-DCB group, log-rank p = 0.895, and three cardiac deaths (11 per 1000 person-years) in the PL-DCB group and ten cardiac deaths (11 per 1000 person-years) in the SP-DCB group, log-rank p = 0.849. Diabetes mellitus under insulin treatment [hazard ratio (HR) 2.71; 95% confidence interval (CI) 1.31–5.60; p = 0.007], chronic kidney disease (HR 1.99; 95% CI 1.01–3.92; p = 0.045), early-onset ISR (HR 1.99; 95% CI 1.18–3.36; p = 0.010), and recurrent ISR (HR 1.89; 95% CI 1.08–3.32; p = 0.026) were associated with the occurrence of MACE after DCB angioplasty. There was no significant difference of MACE between PL-DCB and SP-DCB treatment in patients with ISR. Patients with insulin-treated diabetes, chronic kidney disease, early-onset ISR, and recurrent ISR were at a higher risk of MACE after DCB angioplasty.