Core-binding factor acute myeloid leukemia (CBF-AML) is a subtype of AML characterized by specific genetic rearrangements, including t(8;21) and inv(16), which are associated with a relatively favorable prognosis with relapse rates around 30%. The mutational profiling of CBF-AML is highly heterogeneous in pediatrics, with mutations in the tyrosine kinase pathway (including , and ), epigenetic regulators, cohesin, and additional cytogenetic abnormalities. The identification of high-risk mutations, such as those in and , underscores the need for targeted therapies and highlights the importance of high-throughput sequencing technologies, providing critical insights into the prognosis and informing treatment strategies. Integrating targeted agents with existing treatment protocols has the potential to enhance treatment efficacy and significantly improve patient outcomes. However, CBF-AML presents significant heterogeneity in both pathophysiology and clinical characteristics, with cooperating cytogenetic mutations, leading to difficulties and uncertainties in the prognosis and treatment of CBF-AML in pediatrics. Given the relapse rates and the significant impact of specific mutations on prognosis, there is a critical need for improved risk stratification and personalized treatment approaches in pediatric CBF-AML. Ongoing research and clinical trials focusing on the molecular and genetic profiling of pediatric CBF-AML will be essential for developing more effective and targeted therapies, ultimately improving patient outcomes. This review summarizes the molecular genetics profiling in CBF-AML among pediatrics, targeting its effect and interactions on prognosis and treatment to provide an overview for further research based on mutations among CBF-AML in pediatrics.