Cardiovascular disease, including ischemic heart disease, is a leading cause of death worldwide. Improvement of the secondary prevention of ischemic heart disease is necessary. We established a unique referral system to connect hospitals and outpatient clinics to coordinate care between general practitioners and cardiologists. Here, we evaluated the impact and long-term benefits of our system for ischemic heart disease patients undergoing secondary prevention therapy after percutaneous coronary intervention. This single-center retrospective observational study included 3658 consecutive patients who underwent percutaneous coronary intervention at Shizuoka City Hospital between 2010 and 2019. After percutaneous coronary intervention, patients were considered conventional outpatients (conventional follow-up group) or subjected to our unique referral system (referral system group) at the attending cardiologist’s discretion. To audit compliance of the treatment with the latest Japanese guidelines, we adopted a circulation-type referral system, whereby general practitioners needed to refer registered patients at least once a year, even if no cardiac events occurred. Clinical events in each patient were evaluated. Net adverse clinical events were defined as a combination of major adverse cardiac, cerebrovascular, and major bleeding events. There were 2241 and 1417 patients in the conventional follow-up and referral system groups, with mean follow-ups of 1255 and 1548 days and cumulative net adverse clinical event incidences of 27.6% and 21.5%, respectively. Kaplan–Meier analysis showed that the occurrence of net adverse clinical events was significantly lower in the referral system group than in the conventional follow-up group (log-rank: P<0.001). Univariate and multivariate analyses revealed that the unique referral system was a significant predictor of the net clinical benefits (hazard ratio: 0.56, 95% confidence interval: 0.37–0.83, P = 0.004). This result was consistent after propensity-score matching. In summary, our unique referral system contributed to long-term net clinical benefits for the secondary prevention of ischemic heart disease after percutaneous coronary intervention.