Neurological manifestations of COVID-19 may affect both central and peripheral nervous systems. Unlike in adults, in whom majority of severe cases derive from respiratory complications, neurological involvement is one of the main causes of severe COVID-19 in children. This study aimed to detect viral respiratory pathogens, mainly SARS-CoV-2, in nasopharynx and cerebrospinal fluid samples utilizing qRT-PCR (TaqMan) in a pediatric population in Brazil. We evaluated four children with neurological symptoms and laboratory-confirmed SARS-CoV-2 infection: three presenting with meningoencephalitis and one presenting with Guillain-Barré syndrome. All four patients had mild respiratory symptoms. SARS-CoV-2 RNA was identified in two cerebrospinal fluid samples. SARS-CoV-2 involvement should be considered for differential diagnosis in pediatric cases presenting neurological alterations even if symptoms such as headache, anosmia, or dizziness are absent.