Background The community-acquired respiratory distress syndrome toxin (CARDS), a key exotoxin produced by Mycoplasma pneumoniae, can induce cytopathology. M. pneumoniae pneumonia (MPP) is characterized by ciliary ultrastructural abnormalities. The effect and mechanism of CARDS on ciliary function remain to be fully elucidated. Methods We collected bronchoalveolar lavage fluid (BALF) and analysed the differences in proteomics between patients with MPP and those with other infectious diseases using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Findings We found that ciliary FMRP was down-regulated in BALF from patients with MPP. Together, our findings provide mechanistic insights into understanding the pathogenic mechanisms of CARDS on ciliary function and targeting ciliary FMRP signalling may be a potential therapeutic strategy for treating M. pneumoniae infection.