Thromboangiitis obliterans is also known as Buerger’s disease, and it usually affects small-to-medium-sized arteries and veins of the upper and lower extremities. Although as an atypical course of this disease, bilateral renal artery thrombosis and affection of spermatic cord were reported, there has been no report of penile necrosis due to Buerger’s disease in Korea. We present a case of a 47-year-old man with voiding difficulty and urinary retention due to severely atrophic penis and urethra. The patient’s medical history revealed smoking as much as 50 pack/years, and heavy alcohol consumption. Although the patient had been taking anti-coagulant medication for 2 years after diagnosis of thromboangiitis obliterans, penile necrosis was advanced. The patient could self-void after diversion of the urethra into the perineum.