Abstract: OBJECTIVE To investigate the effect of brain CT examination on the diagnosis of central nervous system infection in children, and to analyze its clinical application value. METHODS A total of 48 cases of children with central nervous system infection in Department of Internal Medicine of our hospital from Jan. 2015 to Apr. 2016 were selected as study objects, and were excluded with severe heart, liver and kidney organic diseases and immune system diseases. Computed tomography (CT) and magnetic resonance imaging (MRI) were carried out after admission, and the brain CT imaging findings in children with central nervous system infection were mainly observed. The clinical comprehensive diagnosis results were chosen as the gold standard and compare the results with MRI examination results, the diagnostic results of brain CT examination were observed, and the clinical application value was comprehensively analyzed. RESULTS In 48 cases of children with central nervous system infection, there were 15 cases of viral encephalitis, 8 cases of tuberculous meningitis, 5 cases of cerebral cysticercosis, and 4 cases of purulent meningitis by CT diagnosis, and the total positive rate was 66.67% (32/48); and 15 cases of viral encephalitis, 10 cases of tuberculous meningitis, 6 cases of cerebral cysticercosis, and 5 cases of purulent meningitis by MRI examination, and the total positive rate was 85.42% (41/48). The differences between the two groups were statistically significant (P<0.05). The diagnostic rate of 25 cases of bacterial infection by CT was 43.48% (10/23), which was lower than 95.65% by MRI(22/23), and the differences between the two groups was statistically significant (P<0.05). The diagnostic rates of 23 cases of viral infection were respectively 88.00%(22/25) and 76.00%(19/25) by CT and MRI respectively, with no significant difference. CONCLUSION CT and MRI are the important clinical examination for central nervous system infection. MRI diagnosis is relatively better effect, and CT can be used with MRI according to the requirement for diagnosis in clinical applications, in order to optimize the diagnostic results.