The frequency and severity of invasive fungal infections have been increasingly recognised and new antifungal therapies have expanded the therapeutic armamentarium available to manage such infections. Antifungal agents comprise a significant portion of antibiotic expenditures at major medical centres, prompting adoption of cost-containment measures and treatment guidelines. This paper reviews available data regarding the costs associated with managing fungal infections, including pharmacoeconomic analyses that have been performed in the setting of documented fungal infections, as well as prophylactic and empiric use of antifungal agents. The challenges of performing such studies are discussed, as well as the limitations of published investigations. Finally, recommendations are made regarding the design and implementation of future pharmacoeconomic analyses that can help establish the true costs of managing invasive fungal infections in at-risk patient populations.