Childhood primary angiitis of the CNS (cPACNS) is a poorly understood, rare, and diagnostically challenging neurologic disease. We describe an unusual and autopsy-confirmed case of cPACNS presenting as vertebrobasilar circulation hemorrhagic strokes in a 4-year-old girl. The presentation and clinical features were inconsistent with primary CNS vasculitis and skewed the diagnosis. Autopsy and histopathological analyses revealed a progressive lymphocytic vasculitis affecting the medium to large vessels of vertebrobasilar circulation and sparing the anterior circulation. It is imperative to raise the index of suspicion for cPACNS in any case of unusual or unexplained neurological presentation, especially in the absence of cerebrovascular risk factors and/or coagulation disorders.