To identify the clinicopathological features of malignant urachal tumor in Japan, and analyze the 5-year overall survival of malignant urachal tumor patients. We used the hospital-based cancer registry data to extract malignant urachal tumor cases that were diagnosed in 2008-2009 and 2012-2015, histologically confirmed, and received the first course of treatment. We analyzed the 5-year overall survival using the 2008-2009 cohort's data. We identified 456 patients, and malignant urachal tumor accounted for 0.4% of all malignant bladder cancers. The median age was 61 years (range 2-97), and 66% were men. The most common histology was adenocarcinoma (80%), followed by urothelial carcinoma (11%) and squamous cell carcinoma (3%). The proportions of patients were: 19% Ta/Tis/T1N0M0, 55% T2-3N0M0, 13% T4/N+ and 13% M+. Regarding the initial treatment, the proportions of surgery alone were 79% and 33% in cases of T3 or less N0M0 and T4/N+, respectively. The proportion of combination therapy including surgery and chemotherapy were 13% and 44% in T2-3N0M0 and T4/N+, respectively. Radiation therapy was not common at any stage. In the 2008-2009 cohort, the 5-year overall survival rate in Ta/Tis/T1N0M0, T2-3N0M0, T4/N+ and M+ were 60%, 64%, 63% and 12%, respectively. Malignant urachal tumors are quite rare in Japan, and most of those without metastasis are likely to be treated by surgery alone, even at advanced stages. A standard of care must be established for malignant urachal tumor patients at advanced stages or with metastasis, as the prognosis of these patients can be poor. © 2019 The Japanese Urological Association.