Multiplex polymerase chain reaction (PCR) allows for the simultaneous detection of the common viral pathogens associated with meningitis or encephalitis. A review of all the pediatric meningitis panel results for the 3 tertiary hospitals across the Eastern Cape Province of South Africa will provide new epidemiological insights into laboratory-detected CSF viruses in the pediatric population in this resource-limited setting. A retrospective cross-sectional review of laboratory data was performed. Results from all the viral meningitis panel PCR tests from the pediatric wards of 3 tertiary hospitals were accessed for the 3-year period from 2015-2017. The main aim of this study was to describe the commonly detected viruses from pediatric CSF samples. A total of 355 pediatric CSF samples were tested, with 88 specimens yielding positive results for one or more viruses. The commonest virus detected was Human gammaherpesvirus 4 (EBV, n = 44), followed by Cytomegalovirus (CMV, n = 18), Human betaherpesvirus-6 (HHV-6, n = 13), Enterovirus (HEV, n = 8), Human alphaherpesvirus 1 (HSV-1, n = 8), Human alphaherpesvirus 3 (VZV, n = 6), Human alphaherpesvirus 2 (HSV-2, n = 2) and Mumps rubulavirus (mumps virus, n = 2). EBV and CMV were the commonest viruses detected, with CMV accounting for half of all viral detections in neonates, whereas EBV predominated among all the other age groups. Interpretation of CSF PCR results may not always be straight-forward, and it is therefore important for clinicians to have some knowledge of the common CSF-detected viruses in their setting.