Candida auris (C. auris) is an emerging fungal pathogen increasingly associated with healthcare-associated infections. Central nervous system (CNS) involvement is rare, and optimal management strategies remain undefined. We report a 13-year-old boy who developed a CNS infection caused by C. auris following firearm-related cranial trauma complicated by dural defect and cerebrospinal fluid (CSF) leakage. Despite systemic antifungal therapy with liposomal amphotericin B and voriconazole, cerebrospinal fluid cultures remained persistently positive. Intrathecal caspofungin was initiated because of ongoing microbiological growth and inflammatory CSF findings. Following initiation of intrathecal caspofungin as an adjunct to ongoing systemic therapy, serial CSF cultures subsequently became negative; no procedure-related adverse effects were documented. However, whether microbiological clearance was attributable to the intrathecal route, the cumulative effect of combination systemic therapy, or both cannot be determined from a single case. Nevertheless, this case underscores the therapeutic challenges of C. auris CNS infections and adds to the limited literature on adjunctive intrathecal caspofungin use in pediatric patients.