Objective To explore the value of FilmArray meningitis/encephalitis (FA ME) panel and metageno-mics next-generation sequencing (mNGS) in pathogenic diagnosis of central nervous system (CNS) infection. Methods Cerebrospinal fluid (CSF) specimens from 29 patients with suspected CNS infection in the Third Affiliated Hospital of Sun Yat-sen University between June 2020 and January 2021 were collected for FA ME panel detection and mNGS, combined with bacterial/fungal culture and viral nucleic acid/serological detection results, effects of FA ME and mNGS in the pathogenic diagnosis of CNS infection were compared. Results The positive rates of FA ME and mNGS were 7.1% and 9.1% respectively, which were slightly higher than 3.4% of bacterial culture, there was no significant difference (P=1.000). In terms of fungi, positive rates of FA ME and mNGS were 10.7% and 13.6% respectively, which were both lower than those in fungal culture (17.2%), difference was significant (P=0.003). The positive rates of virus detected by FA ME and mNGS were 3.6% and 18.2% respectively, which were higher than those detected by nucleic acid/serology in hospital (0). Conclusion FA ME and mNGS are not enough to replace the current routine detection in hospital, but may be used as an adjunctive tool to improve the detection level of CNS infection pathogens.