Objective To investigate the etiological characteristics of bacterial meningitis (BM) in infants aged <90 days. Methods A retrospective analysis was conducted on the etiology and outcomes of BM in infants aged <90 days admitted to five collaborating hospitals between January 2007 and December 2021. The overall etiological profile was described, and pathogen distributions were compared across different age groups, regions, and years. The prognosis of BM caused by common pathogens was also evaluated. Results A total of 197 infants with bacteriologically confirmed BM were included. The most common pathogens were Escherichia coli (E. coli) (72 cases, 36.5%), group B Streptococcus (GBS) (49 cases, 24.9%), and Listeria monocytogenes (LM) (11 cases, 5.6%). The detection rate of E. coli was significantly higher in the neonatal group than in the infant group (40.2% vs 18.2%, P<0.05). E. coli was the predominant pathogen in Beijing (31.7%) and Kunming (54.1%), while GBS and E. coli were equally prevalent in Shenzhen (33.3%). From 2018 to 2021, the detection rates of E. coli were 46.4%, 47.2%, 45.2%, and 36.8%, respectively, whereas those of GBS were 25.0%, 27.8%, 22.6%, and 31.6%. No significant difference was observed in the overall complication rates among BM cases caused by E. coli, GBS, and LM (P>0.05). However, ventriculitis and hydrocephalus were more frequent in LM meningitis than in GBS meningitis (P<0.017). Conclusions E. coli is the most common pathogen in BM among young infants, particularly neonates. GBS is predominant in Shenzhen, with an increasing trend. LM meningitis accounts for a notable proportion of cases and is associated with poorer outcomes.