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Background/Objectives: Penile malignant tumors are rare neoplasms, and both clinicopathologic features and prognoses remain unclear in Japanese patients. Here, we investigated the prognoses of penile malignant tumors in Japan using the nationwide hospital-based cancer registry (HBCR) database. Methods: The 2015 HBCR database cohort was queried to identify patients with penile malignant tumors. Moreover, we investigated age, pathology, tumor-node-metastases classification, first-course treatment, and overall survival in these patients. Results: A total of 269 patients were analyzed from the 2015 cohort (149 squamous cell carcinoma [SCC] patients and 56 extramammary Paget disease [EMPD] patients). The median ages at diagnosis in both SCC and EMPD patients were 76.0 and 76.5 years. The median observation period was 53 months in the present study. The 5-year overall survival (OS) rates of SCC and EMPD were 56.8% and 78.5%. The 5-year OS rates of clinical stages 0-I, II, III, and IV were (respectively) 68.0%, 70.1%, 38.5%, and 11.9% in SCC patients and (respectively) 83.7%, 83.3%, not evaluated, and 0% in patients with EMPD. Conclusions: We revealed the OS of Japanese patients with penile SCC and EMPD in a large population-based study for the first time. Patients with clinical stage IV penile SCC and EMPD had extremely poor prognoses, highlighting a need for improved disease management in these patients.