Visceral leishmaniasis is an endemic in the southwestern region of Saudi Arabia, with a low incidence rate. Clinical presentations of visceral leishmaniasis include recurrent fever, substantial weight loss, hepatosplenomegaly and anemia. However, the clinical features may not be easily evident owing to the involvement of multiple organs. This, in turn, can cause difficulties in establishing the correct diagnosis, and subsequently, in managing the patient. Here, the authors report a case of a 42-year-old male from Jizan, southwestern Saudi Arabia, who presented with impaired renal function. After kidney biopsy, the patient was diagnosed with glomerulonephritis of unknown etiology and treated with mycophenolate and prednisone. After 3 months, the patient developed high fever with hepatomegaly and pancytopenia. Based on the investigations, a possible diagnosis of visceral leishmaniasis was considered. Accordingly, he was treated with liposomal amphotericin B, following which his condition improved significantly. This case report discusses the relationship between glomerulonephritis and visceral leishmaniasis and focuses on the potential consequences of glomerulonephritis management without investigating the etiology of the underlying diseases, especially in patients from tropical and subtropical areas.