Recently, the number of long-term survivors of ≥ 5 years after stomach carcinoma resection is increasing in Japan. The clinical courses of 4,883 patients who underwent stomach carcinoma resection were retrospectively reviewed to investigate the cause of death including multiple primary cancers (MPC) and delayed stomach carcinoma recurrence among long-term survivors of ≥ 5 years. Of 3,061 patients who survived for ≥ 5 years, 1,203 patients (39.3%) were dead after 5 years survival, including 299 patients (24.9%) who died of MPC. Of 84 patients (7.0%) who died of recurrent stomach carcinoma, 25 patients were newly diagnosed ≥ 5 years postoperative. The most common site of MPC was lung in 124 patients, and 347 patients (44.7%) had a smoking-related MPC, including 124 lung, 63 esophagus, 62 head and neck, and 98 other cancers. We examined the prognostic differences in 527 patients with MPC according to the diagnosis time. In 325 patients of long-term survivors in whom MPC was diagnosed ≥ 5 years postoperative, 5-year survival rate and the median survival time after diagnosis were 35.1% and 17.7 months, respectively. This outcome was significantly poorer than that of 160 patients in whom MPC was diagnosed within 5 years postoperative (58.5% and 62.7 months, P < 0.0001). In conclusion, MPC accounted for approximately a quarter of the cause of death in long-term survivors. Lifestyle instructions including smoking cessation are important. Periodical cancer screening allows the early asymptomatic diagnosis and may contribute to a decrease in cancer mortality of MPC in long-term cancer survivors.