Chlamydia psittaci (C. psittaci) pneumonia is a zoonotic infectious disease caused by C. psittaci, which is often underdiagnosed. The application of metagenomic next-generation sequencing (mNGS) provides an unbiased method for the detection of unknown pathogens. A 46-year-old man received empirical treatment with piperacillin-tazobactam and moxifloxacin after an initial diagnosis of prostatitis and pneumonia. However, he experienced recurrent symptoms and a cough, and a chest computed tomography (CT) showed aggravated pulmonary inflammation. Upon further questioning, the patient recalled a history of contact with pigeons, and a bronchoscope alveolar lavage fluid analysis with mNGS suggested C. psittaci infection. Following treatment with doxycycline, the patient's symptoms were rapidly alleviated, and chest CT showed pulmonary lesions absorption. The patient was followed up for 1 month without any discomfort. This case highlights that initial manifestations of C. psittaci pneumonia may present with atypical symptoms such as prostatitis. Furthermore, mNGS can be a useful tool for the detection of rare or unknown pathogens such as C. psittaci.