Several studies have reported an association of autism spectrum disorder (ASD) with central nervous system (CNS) infections and intrauterine infections; however, the results remain unclear. This study aimed to examine this issue using an extensive national database. Utilizing JMDC medical claims database, we conducted a retrospective cohort study of children with at least three years of follow-up from birth, ensuring the mother's information was available. The focus was on the relationship between ASD incidence and exposures like viral meningitis/encephalitis, bacterial meningitis, and intrauterine infections. Cox proportional hazards was used to calculate hazard ratios (HRs) with covariates such as presence of maternal history of mental illness, preterm, low birth weight, respiratory and cardiac disorder, epilepsy, and cranial malformations. Sensitivity analysis was performed on sibling and multiple birth cohorts to adjust for genetic factors. Out of 276,195 mother-child pairs, bacterial meningitis was observed in 1326 (0.5%), viral meningitis/encephalitis in 6066 (2.2%), intrauterine infection in 3722 (1.3%), and ASD in 14,229 (5.2%) children. The adjusted HRs (95% confidence interval, p value) for ASD were 1.40 (1.25-1.57, p < 0.001), 1.14 (1.02-1.26, p = 0.013), and 1.06 (0.87-1.30, p = 0.539) for viral meningitis/encephalitis, intrauterine infection, and bacterial meningitis, respectively. After sensitivity analysis, the HRs for viral meningitis/encephalitis and ASD remained significantly high. Viral meningitis/encephalitis may be an independent risk factor for ASD. Awareness of this risk among healthcare professionals can lead to early intervention and potentially improved outcomes for affected children.