Granulomatosis with polyangiitis (GPA) is an autoimmune small to medium vessel inflammatory vasculitis that can affect multiple organ systems, with predominantly pulmonary, renal and musculoskeletal manifestations. Rarely, there have been cases involving the genitourinary system, particularly causing urethritis and prostatitis. In some incidences, this may mimic prostate abscess or malignancy. We present a case of a 36-year-old man with refractory urinary retention secondary to prostate abscess due to GPA. This case necessitated transurethral resection of the prostate (TURP) and supra-pubic catheterisation, later complicated by a peri-anal abscess and severe urethritis. A potential recto-urethral fistula was noted on magnetic resonance imaging (MRI) and cystourethroscopy, which was managed conservatively with long-term catheter drainage until resolution. The patient ultimately displayed many severe clinical manifestations of a systemic vasculitis and this case report emphasises the importance of considering autoimmune vasculitis conditions as a differential diagnosis when managing inflammatory genitourinary conditions. This case report highlights the importance of obtaining sufficient tissue to make a timely diagnosis in order to initiate immunosuppressant therapy and disease-modifying anti-rheumatic drugs (DMARDs).