Male primary urethral urothelium carcinoma is a rare clinical case. Here, we detail a case of a 58-year-old man with primary urothelium carcinoma of the distal urethra treated in our hospital. The patient with a neoplasm inside the external urethral orifice for 2 years, which was previously diagnosed as condyloma acuminata, had received photodynamic therapy for 3 times, with initial symptoms of urinary stream bifurcation and dysuria. The exfoliative urine cytology showed negative. Cystoscopy showed a tumor growing around the distal urethra. Biopsy and immunohistochemistry revealed high-grade papillary urothelium carcinoma. The patient received partial urethrectomy, followed by urinary bladder irrigation chemotherapy with epirubicin postoperatively. The corpus spongiosum was invaded while the corpus cavernosa were not. Postoperative pathological examination showed high-grade invasive urothelium carcinoma. There is no evidence of tumor recurrence, metastasis or surgical complications during a 61-month follow-up period. Male primary urethral urothelium carcinoma is a rare clinical case with particular clinical and pathological characteristics. There are still no established treatment guidelines and should be studied further.