Hematopoietic transplantation is the preferred treatment for many patients with hematologic malignancies. Some patients may develop invasive fungal diseases (IFDs) during initial chemotherapy, which need to be considered when assessing patients for transplant and treatment post-transplant. Given the associated high risk of relapse and mortality in the post-hematopoietic stem-cell transplant (HSCT) period, IFDs, especially invasive mold diseases, were historically considered a contraindication for HSCT. Over the last 3 decades, advances in antifungal drugs and early diagnosis have improved IFD outcome, and HSCT in patients with recent IFD has become increasingly common. However, an organized approach for transplanting a patient with prior IFD is scarce and decisions are highly individualized. Patient, malignancy, transplant procedure, antifungal treatment, and fungus-specific issues affect the risk of IFD relapse. Effective surveillance to detect IFD relapse post HSCT and careful drug selection for antifungal prophylaxis are of paramount importance. Antifungal drugs have their own toxicities and interact with immunosuppressive drugs such as calcineurin inhibitors. Immune adjunct cytokine or cellular therapy and surgery can be considered in selected cases. In this review, we critically evaluate the aforementioned factors and provide guidance for the complex decision-making of peri-HSCT management of these patients.