Penile glans necrosis is a rare clinical condition caused by trauma, diabetes mellitus, adverse effect of vasoconstrictive solutions, and circumcision. Antiphospholipid syndrome (APS) is categorized as an autoimmune disease with the presence of antiphospholipid antibodies that results in an increased risk of vascular thrombosis and obstetrical complications. In this article, we report a rare case of a 20-year-old boy with penile glans necrosis due to penile vascular thrombosis following catastrophic antiphospholipid syndrome (CAPS) which we successfully treated at People’s Hospital 115.