BACKGROUND: Rectal neuroendocrine neoplasms (NENs) are rare, but their incidence has increased in recent years. The metastasis rate is low in cases of a tumor diameter < 1 cm or depth of invasion lower than the submucosa; therefore, the European Neuroendocrine Tumor Society (ENETS) and the North American Neuroendocrine Tumor Society (NANETS) consensus guidelines recommend endoscopic resection. Since little has been reported on the long-term prognosis of endoscopic resection for rectal NEN, consensus is lacking regarding the follow-up period after endoscopic resection. CASE PRESENTATION: Here, we report three cases of metachronous liver metastasis after long-term follow-up of endoscopic mucosal resection (EMR) for rectal NEN. The pathological findings indicated a depth lower than the submucosa and complete radical resection in all cases and lymphovascular invasion in only one case. All three cases showed metachronous multiple liver metastases after 9-13 years of follow-up for EMR, despite achieving complete resection and without muscular invasion. CONCLUSIONS: Metachronous liver metastases may occur after long interval following endoscopic resection; thus, long-term follow-up is necessary after endoscopic resection for rectal NEN.