IntroductionBasal cell carcinoma of the prostate is rare, with no established treatment for its recurrence or metastasis. We report a case involving basal cell carcinoma of the prostate controlled using radiotherapy.Case presentationA 57‐year‐old man complained of perineal pain. Although his prostate‐specific antigen was 0.657 ng/mL, a digital rectal examination revealed his prostate was stone hard. Prostate needle biopsy showed basal cell carcinoma of the prostate. The patient then underwent radical prostatectomy. Local recurrence and sacral bone metastasis appeared 2 months after surgery. OncoGuide™ NCC Oncopanel System showed deletion ofSMARCB1; however no recommended treatment was identified. Thus, we decided to perform radiotherapy, which reduced all lesions.ConclusionBasal cell carcinoma of the prostate may have a poor prognosis with recurrence or metastasis, hence evaluation of prognostic factors is important. In this case, the genomic profiling test suggested thatSMARCB1deletion may be a prognostic factor associated with disease progression.