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Simple Summary: Invasive fungal infections (IFD) are a significant cause of morbidity and mortality in patients with hematological malignant disorders. The aim of this retrospective study was to investigate the prevalence and outcome of IFD in patients who received cellular therapies. Adult hematopoietic cell transplantation (HCT), chimeric antigen receptor (CAR) T cell, and gene therapy recipients were retrospectively enrolled. We studied 950 patients who received cellular therapies. No CAR T cell and gene therapy patient showed IFD whereas 3/456 autologous HCT recipients who suffered from primary refractory/relapsed lymphomas presented with probable IFD. A total of 11/473 allogeneic HCT recipients developed probable IFD, possible IFD was found in 31/473 and IFD was proven in 10/473. Three patients were reported to have a second episode of IFD. IFDs were associated with poor outcomes in allogeneic HCT recipients. Further studies are needed to improve diagnostics and therapeutics in high-risk populations, such as allogeneic HCT recipients in whom IFD is associated with poor outcomes. (1) Background: Autologous, allogeneic hematopoietic cell transplantation (HCT) and other cellular therapies, including CAR T cell and gene therapy, constitute a cornerstone in the management of various benign and malignant hematological disorders. Invasive fungal infections (IFD) remain a significant cause of morbidity and mortality in HCT recipients. Therefore, we investigated the prevalence and risk factors of IFD following HCT and other cellular therapies in an era of novel antifungal prophylaxis. (2) Methods: In this study, we retrospectively enrolled adult HCT recipients who were treated at our JACIE-accredited center according to standard operating procedures over the last decade (2013–2022). (3) Results: 950 patients who received cellular therapies were studied. None of the 19 CAR T cell and neither of the two gene therapy recipients developed IFD whereas 3/456 autologous HCT recipients who suffered from primary refractory/relapsed lymphomas presented with probable IFD. Overall, 11 patients who received allogeneic HCT experienced probable IFD, possible IFD was found in 31/473, and IFD was proven in 10/473. A second IFD episode was present in three patients. Four-year OS was significantly lower in proven compared to probable IFD (p = 0.041) and was independently associated with HCT-CI (p = 0.040) and chronic GVHD (p = 0.045). (4) Conclusions: In this real-world cohort, the prevalence of proven and probable IFD in an era of novel antifungal prophylaxis was found to be relatively low. However, IFDs were associated with poor outcomes for patients who received allogeneic HCT. [ABSTRACT FROM AUTHOR]