In the present report, we describe the first case of a phaeohyphomycotic brain abscess in a 5-year-old boy with chronic granulomatous disease (CGD) admitted to hospital with seizures. A computed tomography (CT) scan revealed a cerebral abscess and the microbiology study showed a dark, melanin-pigmented fungus, exhibiting only sterile hyphae. This fungus was identified by the amplification and sequencing of the 5.8S RNA gene and of the adjacent internal transcriber spacer domains, ITS1 and ITS2, as Alternaria infectoria. Due to the impossibility of a surgical excision, and although several therapeutic strategies were attempted, the patient died. Limitations in the routine identification procedures and therapeutic options of this emerging opportunistic agent are highlighted in this report.