Percutaneous coronary intervention (PCI) with drug-coated balloons (DCB) or drug-eluting stents (DES) are well-established treatments for in-stent restenosis, however little is known about the impact of vessel size on the outcomes. The study aimed to evaluate the efficacy and safety profile of DCB versus DES in DES in-stent restenosis depending on the vessel size. Consecutive patients with DES in-stent restenosis who underwent PCI between January 2010 and February 2018 entered the registry with a long-term follow-up. Patients who received DCB at the index procedure were compared with those who received DES in three subgroups depending on the vessel size (≤2.5 mm; 2.5-3.5 mm; >3.5 mm). Data were analyzed using propensity score matching and Kaplan-Meier estimator plots. Among 1,374 patients with DES in-stent restenosis, 615 were treated with DES and 759 with DCB. After propensity score matching, we analyzed 752 patients in the DES and DCB groups at a long-term follow-up. The risk of DOCE did not differ significantly between the DES and DCB groups, both in the overall population (HR 0.85; 95%CI [0.58; 1.26], log-rank p = 0.41) and when divided into small (HR 0.84; 95%CI [0.36; 1.95], log-rank p = 0.70), medium-sized (HR 0.90; 95%CI [0.49; 1.65], log-rank p = 0.73), and large-sized (HR 0.81; 95%CI [0.42; 1.53], log-rank p = 0.50) coronary arteries. The incidence of all-cause death was significantly higher in the overall DES population (HR 4.03; 95%CI [2.40; 6.79], log-rank p < 0.001) and subgroup of small (HR 5.54; 95%CI [1.80; 17.02], log-rank p = 0.003), medium-sized (HR 4.37; 95%CI [1.92; 9.94], log-rank p = 0.009) and large-sized coronary arteries (HR 3.26; 95%CI [1.35; 7.86], log-rank p = 0.02). DES and DCB strategies are comparable methods of treating ISR regardless of the diameter of the treated vessel in a long-term follow-up.