Scedosporium boydii is considered an opportunist fungal pathogen in immunocompromised patients. It also causes serious and fatal central nervous system infections. In this study, a man with brain abscesses infected with S. boydii was diagnosed using multiple methods, including microscopy, culture combined with Matrix‐assisted laser desorption ionization time‐of‐flight mass spectrometry (MOLDI‐TOF MS), internal transcribed spacer sequencing and Metagenomic next‐generation sequencing (mNGS). This successful diagnosis highlights the importance of using a variety of techniques to identify and treat infections caused by this dangerous fungus.