This retrospective analysis reviews the laboratory and clinical data of two infants with visceral leishmaniasis treated at Kunming Children’s Hospital from January 2021 to December 2022. Both patients were female from Yunnan, and 9 months and 2 years old, respectively, with a history of residence in endemic areas (Gannan Tibetan Autonomous Prefecture, Gansu Province, and Kuqa City, Xinjiang Uygur Autonomous Region) and a history of sandfly bites. Symptoms included irregular fever (39.7 ℃ to 40 ℃), rash, and pallor. Blood routine tests showed decreased white blood cells (3.92 × 10⁹/L, 3.34 × 10⁹/L), hemoglobin (98 g/L, 79 g/L), and platelets (49 × 10⁹/L, 57 × 10⁹/L), with elevated C-reactive protein (200 mg/L, 58.19 mg/L), procalcitonin (2.29 ng/ml, 1.38 ng/ml), and ferritin (69 445 µg/L, 2 800 µg/L). rK39 antibody tests were positive. Bone marrow smears revealed Leishmania amastigotes. The second case,through comprehensive pathogen metagenomic next-generation sequencing, identified 32 026 sequences of Leishmania donovani. Abdominal ultrasound showed hepatosplenomegaly in both patients. After diagnosis, sodium stibogluconate was administered at 240 mg/kg divided into 6 doses, with one intravenous injection per day. It resulted in a cure, with no abnormalities at six months and one year follow-up. Visceral leishmaniasis in children can have atypical symptoms. If there is prolonged irregular fever, clinicians should inquire in detail about the epidemiological history of visceral leishmaniasis. Metagenomic sequencing may be necessary to avoid misdiagnosis or missed diagnosis if no pathogens are found in the bone marrow.