INTRODUCTION: Visceral leishmaniasis (VL) is a parasitic disease caused by various Leishmania species and is a potentially life-threatening condition. The disease is highly endemic in several regions, including the Balkans, yet information regarding its prevalence in Kosovo is limited. CASE PRESENTATION: In this case presentation, a 62-year-old man was admitted to a hospital in Kosovo due to a persistent high fever, and after extensive evaluations and treatments, he was diagnosed with fever of unknown origin (FUO) and transferred to a hospital in Turkey. An abscess of the psoas muscle caused by MRSA was found, however, pancytopenia persisted despite antibiotic treatment. Six months later, the patient was hospitalized again due to fever, chills, and night sweats. Microscopic examination and serological tests revealed the presence of Leishmania infantum in the bone marrow. Liposomal amphotericin B treatment resulted in a significant improvement in the patient's condition. DISCUSSION: The diagnosis of VL can be challenging, and it can easily be misdiagnosed as other diseases, resulting in diagnostic delays and potentially fatal outcomes. In endemic regions such as the Balkans, it is crucial for physicians to be aware of this infection to avoid misdiagnosis or diagnostic delay. Early diagnosis and prompt treatment of VL are essential in preventing morbidity and mortality. CONCLUSION: This case highlights the significance of considering VL as a possible diagnosis in patients presenting with febrile illnesses accompanied by pancytopenia and splenomegaly, especially in endemic regions.