Herein, we report the use of microdochectomy for neuroendocrine ductal carcinoma in situ( NE-DCIS). The patient was 44-year-old woman who experienced spontaneous nipple discharge for 5 years. We were unable to detect the origin of the nipple discharge by computed tomography (CT), magnetic resonance imaging (MRI), mammography, ductal endoscopy, or ultrasonography. Subsequently, endoscopy-assisted microdochectomy was performed under local anesthesia. Pathological examination of the resected specimen led to a diagnosis of NE-DCIS positive for estrogen and progesterone receptors and negative for HER2/neu protein expression. The Ki-67 positive cell index was 80%. The surgical margins were negative. After surgery, tamoxifen was administered. One year after the operation, the patient is well and metastases have not been noted. This case suggests that endoscopy-assisted microdochectomy under local anesthesia is useful for evaluating spontaneous nipple discharge.