Gardnerella vaginalis is a pathogen responsible for bacterial vaginosis, which is commonly found in female vaginas and rarely causes infections outside the female genitalia. Here, we report the use of metagenomic next-generation sequencing (mNGS) to detect and confirm pulmonary infection and pleural effusion caused by G. vaginalis in a 47-year-old man. The patient's symptoms and imaging improved after 2 weeks of oral ornidazole, and he was cured after 3 months. Overall, the findings of this case demonstrate that mNGS is a useful tool for diagnosis of unexplained lung infections and pleural effusions. Its effectiveness in rapid and accurate etiological diagnosis and monitoring of diseases can allow detection of the etiology of difficult cases that return negative results after traditional cultures.