Aspergillus fumigatus infections are increasing in incidence and are associated with high mortality rates, high cost of treatment and longer hospital stays. In addition, the limitations of current effective antifungals and increasing antifungal resistance highlight the need for the development of new antifungals with novel targets. Thioredoxin reductase (TrxR) catalyses the reduction of thioredoxin by NADPH, and is responsible for maintenance of intracellular redox homeostasis and providing reducing equivalents to various biosynthetic enzymes. The importance of TrxR for normal cellular function in addition to considerable structural and mechanistic differences between the fungal and human enzymes present TrxR as a promising target for novel antifungals. Ebselen (2-phenyl-1,2-benzoselenazol-3-one) has been shown previously to interact with TrxR, acting as a substrate for human TrxR, but as an inhibitor of bacterial TrxR. Here, we present the structure of A. fumigatus TrxR in complex with FAD and NADPH, solved to 3.2 Å, and show that Ebselen is a potent inhibitor of the enzyme in vitro. We also show that Ebselen inhibits growth of A. fumigatus in culture with an MIC of 1-2 µg/mL. Mass spectrometry analysis demonstrates that Ebselen interacts covalently with a specific catalytic cysteine, Cys148, at the TrxR active site. In silico studies of the enzyme in complex with Ebselen define molecular interactions which are important for inhibition of the enzyme, providing a scaffold for future design of specific and potent anti-Aspergillus drugs that target TrxR.