Scedosporium apiospermum is a filamentous fungi that commonly causes cutaneous infection. In certain circumstances, S. apiospermum can also cause invasive disease, which can involve the central nervous system (CNS). When the CNS becomes involved, treatment is difficult, therapeutic options are limited and the prognosis is poor. Early identification and treatment can decrease the mortality rate. Here we present a case of brain abscess with chronic suppurative otitis media, caused by S. apiospermum. This is the first such case report from Nepal. We could identify the organism only post mortem. We could not save the patient, probably due to delay in diagnosis.