In this study, autopsy samples were obtained and analyzed from 33 individuals infected with SARS-CoV-2, which were either confirmed by RT-qPCR or strongly suggestive from clinical presentation. Clinical and post-mortem records indicated neurological alteration, including impaired consciousness, intraventricular hemorrhage, headache, behaviour change, acute cerebral ischemia, and acute infarcts. SARS-CoV-2 RNA and proteins were present in nasopharynx and brain samples. More specifically, viral RNA levels were highest in the olfactory mucosa, and neural-mucosal interface appeared to serve as an entry point to the central nervous system (CNS), which affects smell and taste. Other findings included inflammation in CNS due to upregulation of macrophages, histopathological evidence of cerebral micro-thrombosis and acute infarct in 18% of individuals, and thromboembolic ischemic infarction of CNS due to infection and SARS-CoV-2 neurotropism. The results of this study help explain COVID-19’s neurological consequences in cases that have resulted in death.