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Fungal siderophores play a significant role in iron transport into the fungal cell as the latter requires exogenous iron for its survival. The chemistry and biomedical applications of fungal siderophores are reviewed here. The biosynthesis of fungal siderophores starts with L-ornithine and hydroxamate moiety is present in most of the fungal siderophores and subsequently they belong to hydroxamate type. Chemical structure-wise, they are classified into three major families, namely, coprogens, fusarinines and ferrichromes. The biomedical applications of fungal siderophores include antidote for iron overload conditions, antimicrobial agent by using Trojan horse strategy, medical imaging and biosensor platforms. The Trojan horse strategy appears to be promising against drug-resistant invasive fungal infections.