Invasive fungal infections are associated with significant morbidity and mortality. Differences between children and adults are reported, yet few trials of antifungal agents have been performed in pediatric populations. We performed a systematic review of the literature to guide appropriate pediatric treatment recommendations. From available trials that compared antifungal agents in either prolonged febrile neutropenia or invasive candidal or Aspergillus infection, no clear difference in treatment efficacy was demonstrated, although few trials were adequately powered. Differing antifungal pharmacokinetics between children and adults were demonstrated, requiring dose modification. Significant differences in toxicity, particularly nephrotoxicity, were identified between classes of antifungal agents. Therapy needs to be guided by the pathogen or suspected pathogens, the degree of immunosuppression, comorbidities (particularly renal dysfunction), concurrent nephrotoxins, and the expected length of therapy.