Visceral leishmaniasis (VL) is a systemic protozoan infection caused by Leishmania donovani (L. donovani) and transmitted by sand flies, causing macrophage invasion in the liver, spleen, and bone marrow. Diagnosis of VL is currently based on clinical signs, symptoms, and specific in-vitro markers and bone marrow investigations. However, VL's specific hematological and bone marrow manifestation in Sudanese pediatric patients is not well studied. To examine the blood and bone marrow characteristics in pediatric patients from Sudan who have VL. This is a retrospective hospital-based study with a sample of 107 consecutive Sudanese pediatric patients. The data focused on hematological and bone marrow results. We included only the completed records of the pediatric patients with VL in the Tropical Disease Teaching Hospital in Khartoum, Sudan from the period of 2016 to 2020. The majority of pediatric patients included in this study are below 5-years-old (n = 59, 55.2%). Moreover, anemia, thrombocytopenia, and leukopenia were among the prevalent characteristics in the population under study. To further analyze the data, we developed a machine learning model using boosted forest algorithms to predict L. donovani parasites load, with a mean accuracy of 0.88 for the training dataset and an accuracy of 0.46, 0.50, and 0.74 for mild, moderate, and severe L. donovani parasite load in the validation dataset. This study shows that the most common bone marrow change among Sudanese VL children was increased chronic inflammatory cells (n = 88, 82.2%) with present macrophage hemophagocytes (n = 103, 96.3%). While anemia and thrombocytopenia were the most common hematological changes. These results will hopefully lead to an early diagnosis and hence better management for Sudanese pediatric patients with suspected VL.