Neuroendocrine carcinomas of the anal canal are rare, representing 1% of malignant tumors of the anal canal. This tumor behaves aggressively and leads to poor outcomes. The majority of tumors are found with distant metastases. We describe the case of a 63-year-old female with T1 neuroendocrine carcinoma of the anal canal arising from the site of a previous transanal excision performed 13 months earlier for intramucosal adenocarcinoma of the anal canal. The patient did not have any distant metastases on preoperative computed tomography and magnetic resonance imaging. She underwent abdominoperineal resection after the initial diagnostic transanal excision of the neuroendocrine carcinoma, which had shown submucosal invasion. No lymph node metastasis was found in pathological examination. In this case, it is likely that the neuroendocrine tumor, which infiltrated into the submucosal layer with venous invasion, had developed over the intervening 13 months following the original transanal excision of the adenocarcinoma.