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Scientific evidence from public health findings can enhance the management, treatment, and prevention policies for bacterial meningitis (BM) infections. However, comprehensive epidemiological data on BM prevalence in South Africa is limited. We aimed to assess the prevalence and characteristics of laboratory-confirmed BM cases at the national population level. Using PRISMA standards, we retrieved data from electronic databases and selected reference articles. Out of 115,626 participants, 57,964 (50.13%) were infected with BM, with the highest prevalence (7.67%) in the age group 6–17 years. Our meta-analysis of 19 studies revealed an overall pooled prevalence of 38.01%, 95% confidence interval (CI: 0.26–0.50), with significant heterogeneity (I² = 99.86%, Q = 13117.45, p < 0.0001). The Egger test indicated publication bias (z = 3.4977, p = 0.0005). Subgroup analyses showed a higher prevalence in studies with sample sizes over 1000 (60.22%, 95% CI: 0.3899–0.7819, I² = 99.92%), over long study years (37.50%, 95% CI: 0.2642–0.5005, I² = 99.84%), cross-sectional study design (58.69%, 95%CI: 0.4906–0.6770, I2 = 99.72%), and particularly in Gauteng province (60.42%, 95% CI: 0.4539–0.7371, I² = 98.45%). The infectious types included Listeria (83.33%, 95% CI: 0.1936–0.9905, I² = 0.00%) and Neisseria (62.64%, 95% CI: 0.6126-0.6400, I² = 0.00%). Significant heterogeneity was noted in study design (R² = 52.93%, p < 0.0001), sample size (R² = 0.00%, p = 0.0117), and province (R² = 0.0%, p < 0.0001). These findings underscore a high prevalence of BM infections in South Africa’s epidemiological landscape, highlighting the urgent need for targeted surveillance for effective prevention and treatment strategies.