We report a case of clear cell carcinoma occurring in the prostate with Zinner syndrome in a 64-year-old man. Based on the immunohistochemical findings, it was concluded that this tumor represented primary renal-type clear cell carcinoma arising in the prostate. After receiving radical cystoprostatectomy, he was treated with tyrosine kinase inhibitor (TKI) therapy for local recurrence in accordance with the protocol of renal cell carcinoma (RCC) treatment, because microarray cluster analysis using a resected sample demonstrated that the present case belonged to the cluster group of RCC.