Syphilis is a sexually transmitted infectious disease caused by Treponema pallidum. Here, we report a rare case of secondary pulmonary syphilis, which was diagnosed by metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF). Direct pulmonary involvement by T. pallidum was suggested by a positive mNGS result in BALF. One month after treatment with benzathine penicillin G (2.4 million units, three doses), a repeated CT scan showed the radiological resolution. To our knowledge, this is the first reported case of secondary pulmonary syphilis diagnosed by mNGS in BALF.