The prevention and treatment of pediatric fungal infections are limited by the fact that not all antifungal drugs are approved for the pediatric age and appropriate dosages have not been established for each age group. The management of neonates and infants with invasive fungal infection is becoming more complex with an increasing number of antifungal agents available. Dosing information, is not available for newer antifungals and is limited with older antifungal agents. Insufficient neonatal studies have been performed with newer agents and there are numerous differences between neonates, children and adults with invasive fungal infection. Kinetic parameters such as the half-life [t1/2], clearance [CL], and volume of distribution [Vd] change with development, therefore the kinetics of antifungals need to be studied in order to optimize therapy with these drugs. A reasonable aim of pediatric dosing is to ensure levels of drug exposure which are comparable to those achievable in adults and which approximate those for which antifungal efficacy has been established. Therefore it will be of clinical relevance to ascertain the dosages of antifungals which produce an equivalent magnitude of exposure to that observed in adults. Drug therapy, studies on prescription and dosing should consider differences between neonates, infants and toddlers, children and adolescents in terms of drug disposition: absorption, metabolism and elimination/excretion. Determining the safety and pharmacokinetics of antifungals in neonates addresses an unfulfilled medical need given that data are sparse in neonates; at present, reports of antifungal pharmacokinetics in the treatment of neonatal fungal infections are limited to case series. The aim of this article is to review the pharmacokinetics of old and new antifungal drugs in neonates and young infants in a single article in order to provide a critical analysis of the literature. It will be important to evaluate all newly developed antifungals in neonates and infants to assure their maximum efficacy and safety. More pharmacokinetic data are required to ensure that the dose recommended for the treatment of fungal infections in the neonate achieves evidence based medicine.