Two infants developed encephalitis in the late neonatal period due to human parechovirus type 3 (HPeV-3). This finally resulted in intractable seizures leading to death. Both presented with classical signs and symptoms. HPeV-3 was detected in nasopharyngeal and rectal swabs, cerebrospinal fluid, serum and postmortem samples (for one infant). Ultrasound and magnetic resonance imaging findings showed severe white matter injury in one infant, and limited hippocampal injury in the other. Parents consented to autopsy in the latter, showing diffuse gliotic oedema of cerebral white matter, bilateral bronchopneumonia, and inflammation in spleen. We emphasise that polymerase chain reaction (PCR) testing for parechovirus in neonates with severe sepsis-like syndrome and meningoencephalitis is mandatory.