Visceral leishmaniasis (VL) is a parasitic disease that can trigger haemophagocytic syndrome (HPS), making its prompt diagnosis crucial. The application of metagenome next-generation sequencing (mNGS) provides a rapid diagnostic approach, particularly for patients with negative bone marrow aspiration results. We present here, a case of a male patient in his early 50s who presented with fever and abdominal pain. Routine examinations failed to identify its specific cause. However, diagnosis through mNGS helped prevent a potentially fatal outcome.