BackgroundPediatric and young adult patients undergoing autologous hematopoietic stem cell transplant (auto‐HSCT) face a crucial, yet understudied, risk of invasive fungal infections (IFI), especially compared to allogeneic transplants. This gap underscores the need for research in pediatric patients undergoing auto‐HSCT. Our objective was to evaluate the incidence of IFI in pediatric and young adult patients during the first year after auto‐HSCT.Materials and methodsWe conducted a single‐center retrospective analysis of 150 pediatric and young adult auto‐HSCT patients who underwent transplant from January 2013 to January 2023. We focused on IFI incidence within the first‐year post transplant, using the European Organization for Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG) criteria for IFI identification.ResultsAmong the 150 patients analyzed, with 240 unique transplant episodes, the primary indication was neuroblastoma (37.3%), and micafungin was extensively used for prophylaxis (82.7%). There was an absence of IFI from yeast and mold species, suggesting a low IFI risk in this cohort. The incidence of IFI in pediatric auto‐HSCT recipients receiving micafungin primary antifungal prophylaxis is rare.ConclusionsThe findings advocate for further research to refine prophylaxis guidelines and highlight the need for individualized risk assessment to optimize post‐transplant care.