Background: Invasive fungal diseases (IFD) are important causes of mortality in children with cancer. We aimed to determine the extent of survival in patients treated for IFD in the last nine years at our center. Procedure: a retrospective cohort of patients treated from January 1, 2011 to December 31, 2019. Weibull distribution was used to parameterize hazard ratios and accelerated failure time models, for the outcome “death attributed to IFD”. Results: We analyzed 152 patients with IFD (133 proven and 19 probable), with median age of 97 months. The most frequent diagnoses were leukemia (39, 25.7%) and central nervous system tumors (36, 23.7%). Thirty-seven patients received prophylaxis with fluconazole (24.3%). There were 133 fungi isolates, and most frequent were Candida species in blood (84, 55.2%). Forty-three deaths were attributed to IFD (28.3%). Survival probabilities were lower for pulmonary IFD (46.9%, p = 0.0017), leukemia (62.5%, p = 0.004), and neutropenia <500 cells/mm3 (55.4%, p < 0.0001). For Candida fungemia, survival probabilities were 76.6% (p = 0.043). In Weibull models, diagnosis of leukemia shortened survival times by a factor of 0.006, relapse of disease by 0.05, lymphoma by 0.04, pulmonary IFD by 0.04, and neutropenia by 0.015. Hematopoietic stem cell transplantation did not affect the survival times, as well as prophylaxis with fluconazole. Conclusions: Host factors, like neutropenia, relapse of disease and hematologic malignancies, are determinant in the survival times of children with IFD, as well as pulmonary involvement. Fluconazole prophylaxis and HSCT do not affect the hazards of death.