A definitive conclusion regarding whether on-pump or off-pump coronary artery bypass is preferable in young patients is lacking. The aim of our study was to perform a long-term comparison of the two approaches in young patients. We analyzed the National Health Insurance Research Database, using data for patients between 18 and 45 years of age who had undergone isolated coronary artery bypass between 2001 and 2011. The study endpoints were: all-cause death, major adverse cardiac and cerebrovascular events, and repeat revascularization within 30 days, 1 year, 5 years, and the entire 10-year follow-up period. A total of 344 patients received off-pump surgery and 741 patients received on-pump surgery. Preoperative characteristics and comorbidities were similar in both groups, and all-cause mortality was almost equal (p = 0.716). The 5-year survival rates were 93.9% and 92.2% in the off-pump and on-pump groups, respectively, and the 10-year survival rates were 86.3% and 82.1%, respectively. The repeat revascularization rate was significantly lower in the on-pump group (p = 0.0407). Both the on-pump and off-pump methods offer equally good long-term outcomes in terms of mortality and major adverse cardiac and cerebrovascular events. However, the need for repeat revascularization is a concern in the long term after off-pump surgery.