Background: Children with hematologic malignancies, especially those who receive intensive chemotherapy, are at high risk for invasive mold infections (IMI) that confer substantial mortality. Randomized controlled trials support the use of anti-fungal prophylaxis with anti-mold activity as an optimal strategy for risk reduction in this population, but studies outlining the practical application of evidence-based recommendations are lacking. Procedure: We conducted a 15-year, single-institution retrospective review of children with hematologic malignancies treated with chemotherapy to determine the incidence of proven or probable IMI diagnosed between 2006 and 2020 and to identify the host and disease factors associated with IMI risk. We then compared the incidence and type of IMI and related factors before and after 2016 implementation of an evidence-based, risk-adapted anti-fungal prophylaxis algorithm that broadened coverage to include molds in patients at highest risk for IMI. Multivariable linear regression was used to determine factors related to IMI risk. Results: We identified 61 cases of proven or probable IMI in 1,456 patients diagnosed with hematologic malignancies during the study period (4.2%). Implementation of an anti-fungal prophylaxis algorithm reduced the IMI incidence in this population from 4.8% to 2.9%. After multivariable analysis, both Hispanic ethnicity and cancer diagnosis prior to 2016 were significantly associated with risk for IMI. Conclusion: An evidence-based, risk-adapted approach to anti-fungal prophylaxis for children with hematologic malignancies is an effective strategy to reduce incidence of IMI.