This paper reports a case of imported visceral leishmaniasis (VL; also known as kala-azar) in a nonendemic area (Wuhan). The patient was a 63-year-old male who had recurrent fever for more than 5 months and failed to respond to multiple treatments for hemophagocytic syndrome (HLH). No pathogen was detected by traditional bone marrow aspiration smear microscopy. Finally, 12347 standardized sequence count of Leishmania species complex were detected in peripheral blood via metagenomic next-generation sequencing (mNGS), confirming the diagnosis of VL. The patient's condition was relieved after treatment with liposomal amphotericin B. This case suggests that mNGS should be used as a powerful tool for early pathogen screening in patients with fever of unknown origin accompanied by HLH in non-endemic areas.