Hymenolepis diminuta is a common parasite of rats and mice, but is very rare in humans with cases reported from various parts of the world. Here, we reported a case of Hymenolepis diminuta infection involving both the respiratory and digestive tracts in a 49-year-old male patient whose initial imaging and symptoms were strikingly similar to pneumonia. Since no disease-causing pathogens were found during routine examinations, we considered respiratory infection by specific pathogens before metagenomic next-generation sequencing of broncho-alveolar lavage fluid confirmed the diagnosis of Hymenolepis diminuta . After confirming the diagnosis, we retested the patient's stool repeatedly and found Hymenolepis diminuta eggs finally. To help doctors better understand this condition and avoid misdiagnosis, this article provided a summary of the clinical characteristics, diagnostic techniques, and therapeutic options for infection by Hymenolepis diminuta .