Our study aimed to compare the efficacy of seal-wing paclitaxel-eluting balloon catheters (PEB) with iopromide-coated PEB and everolimus-eluting stents (EES) for treating bare metal stent restenosis (BMS-ISR). We enrolled 64 patients with 69 BMS-ISR. The control group comprised patients from the iopromide-PEB and EES arms of a previous TIS study. The primary end-point was 12-month in-segment late lumen loss (LLL). Secondary end-points included incidence of binary in-stent restenosis and 12-month major adverse cardiac events (MACE). Compared to iopromide-coated PEB, seal-wing PEB was associated with significantly higher 12-month LLL (0.30 vs. 0.02 mm; p < 0.0001), repeated binary restenosis (28.12% vs. 8.7%; p = 0.012), 12-month MACE (26.98% vs. 10.29%; p = 0.003), and target vessel revascularization (TVR; 20.63% vs. 7.35%; p = 0.009). Compared to EES, no significant differences were found in the 12-month LLL (0.30 vs. 0.19 mm; p = 1.000), repeated binary restenosis (28.12% vs. 19.12%; p = 0.666), 12-month MACE (26.98% vs. 19.12%; p = 0.102) or TVR (20.63% vs. 16.18%; p = 0.360). BMS-ISR treatment using seal-wing PEB led to significantly higher 12-month LLL, repeated binary restenosis, MACE, and TVR compared to iopromide-coated PEB. However, no significant differences were found in comparison with EES. ClinicalTrials.gov; NCT01735825.