Cerebral phaeohyphomycosis is an infrequent infectious condition associated with a high mortality rate. The authors describe a very rare case that occurred in an immunocompetent 18-year-old man who developed severe meningoencephalitis and arachnoiditis caused by Alternaria alternata, which were diagnosed in the context of difficult-to-treat hydrocephalus. Etiological diagnosis was made based on fungal culture and histopathologic examination. Empirical treatment consisted of an early aggressive antifungal combination therapy consisting of intravenous liposomal amphotericin B (5 mg/kg per day) and voriconazole (4 mg/kg every 12 h), which initially induced a favorable response. Following the fungus identification, the choice for the combination of posaconazole (400 mg every 12 h) plus flucytosine (4000 mg/day) proved to be effective in the suppression of the signs and symptoms of this uncommon cerebral mycosis. At a 12-month follow-up visit no recurrence had occurred and posaconazole was then stopped.