We report about a rare case of malakoplakia in a female urethral diverticulum. A 25-year-old patient with a long history of recurrent urinary tract infections and a plum-sized, painful swelling on the vaginal roof presented for operative treatment. In the anamnesis the patient reported about two spontaneous perforations, emptying several millilitres of pus each time. After total operative excision using a vaginal approach the histology showed malakoplakia in a urethral diverticulum. We found the typical intracytoplasmatic "Michaelis-Gutmann bodies" as well as "von Hansemann cells". Postoperatively we excluded an underlying tumour disease or a chronic infection. The further urological diagnostics (cystoscopy and MRI) were without any pathological findings. In patients with atypical cystic tumours of the urogenital tract, especially with an immune deficiency, malakoplakia should be taken in consideration. The preferred therapy is surgical management followed by long-term antibiosis as well as a close follow-up as recurrences are frequent.