Background: Visceral leishmaniasis (VL) is fatal neglected parasitic illness caused by Leishmania donovani. The diagnosis remains a challenge due to the non-specific clinical symptoms, especially in areas where infections like malaria and limited access to diagnostic tools coexist. Here, we describe a case of late diagnosis of visceral leishmaniasis using tru-cut biopsy of the spleen and malaria co-infection. Case Presentation: Here case report, a 24-year-old patient from an endemic region of Somalia presented with fever, headache, abdominal pain, nausea, vomiting, and weight loss for two months. Initially, the patient received symptomatic treatment and a blood transfusion but showed no improvement. Physical examination revealed fever, pallor, and hepatosplenomegaly. Laboratory tests showed pancytopenia and positive rapid diagnostic test for plasmodium parasite antigen. Despite three days of anti-malarial treatment, the symptoms persisted, and hepatosplenomegaly worsened. Further investigations, including infectious disease tests, were conducted, ruling out HIV, viral hepatitis, Brucella, and Leishmania antibodies. Peripheral blood smear showed pancytopenia and bone marrow aspiration revealed no evidence of infection or malignancy. A tru-cut biopsy of the spleen was performed, confirming the diagnosis of visceral leishmaniasis. The patient received a combination therapy of sodium stibogluconate and paromomycin, leading to significant improvement. After completing treatment, the patient was discharged with normal spleen biopsy results. Conclusion: Visceral leishmaniasis (VL) is a challenging disease to diagnose, especially in areas where it coexists with other infectious diseases, such as malaria. Co-infection with malaria should also be considered in patients with fever and hepatosplenomegaly. A high index of suspicion is necessary for the timely diagnosis of VL, and a tru-cut biopsy of the spleen can be conducted in cases where other investigations are inconclusive in endemic areas. Early diagnosis and prompt treatment of visceral leishmaniasis are crucial to prevent complications and reduce mortality.