Apocrine carcinoma is a rare malignant adnexal neoplasm. The differential diagnosis between apocrine carcinoma and cutaneous metastasis is often difficult. Here, we report a case of locally recurrent penile apocrine carcinoma initially diagnosed as metastatic adenocarcinoma of the colon. A 75-year-old man with a history of surgical resection due to sigmoid colon cancer and penile metastasis two years prior to this study presented with a nodule at the left penile base. He underwent a wide local resection of the penile mass under a suggested preoperative diagnosis of extra-mammary Paget’s disease (EMPD) associated with previous sigmoid colon cancer. However, the previously and currently resected penile masses were identified as primary apocrine carcinoma upon hematoxylin and eosin (H&E) staining and immunohistochemical staining. Although the incidence is extremely rare, both clinicians and pathologists should be alert to the possibility of synchronous double primary apocrine carcinoma in cancer patients with malignant cutaneous lesions.