Background: CNS infections have been suggested as risk factors for cognitive decline and mental disorders; however, large-scale studies have been lacking regarding types and agents of CNS infections. Methods: We utilized the unique personal registration number to create a cohort of 1,709,867 individuals born 1977–2010. CNS infection was exposure and data were analysed with 1) cox regression analyses estimating hazard ratios (HR) for developing mental disorders and 2) binomial regression estimating relative risk (RR) for completion of 9th grade including average grade score in a sub-cohort born 1988–1998. Results: CNS infection increased the risk for developing mental disorders with a HR of 1.34 (95% CI 1.27–1.42). The highest risk observed was within the first 6 months after the CNS infection with a HR of 26.98 (95% CI 21.19–34.35). Viral CNS infections (HR 1.47, 95% CI 1.35–1.61) conferred a higher risk (p < 0.001) than bacterial (HR 1.24, 95% CI 1.15–1.35). Encephalitis (HR 1.64, 95% CI 1.41–1.90) conferred a higher risk (p < 0.001) than meningitis (HR 1.26, 95% CI 1.18–1.35). The risk was highest for organic mental disorders (HR 6.50, 95% CI 5.11–8.28) and disorders of intellectual development (HR 3.56, 95% CI 2.94–4.31), with a HR of 19.19 (95% CI 7.46–49.35) for profound disorder of intellectual development (IQ < 20). Furthermore, CNS infection decreased the RR of completing 9th grade of mandatory schooling (RR 0.89, 95% CI 0.88–0.91) and lowered average grade score for completers (p < 0.001). Conclusions: CNS infections increased the risk for mental disorders and decreased the likelihood of completing 9th grade, indicating long-term consequences of CNS infections.