Herein we present a previously unreported rare case of mucinous adenocarcinoma arising from a congenital ejaculatory duct cyst. Radiographic and endoscopic examinations revealed the tumor occurred in a cyst running through the prostate. Initially, the immunohistochemical pathology results showed that it was a metastatic mucinous adenocarcinoma, but no other primary lesions were clinically evidenced. Based on the embryonic development process of the male urogenital tract, the malformation of the patient's ejaculatory duct, and the pathological examination of the resected specimen, we considered the tumor to be a primary mucinous adenocarcinoma which originating from the hypoplastic ejaculatory duct. The tumor may have developed from the foci of intestinal metaplasia from cloacal remnants during embryonic development.