Marfan syndrome (MFS) is a connective tissue disorder caused by mutations in the fibrillin-1 gene. Acute lymphoblastic leukemia (ALL) is the most common childhood cancer. The coexistence of MFS and ALL is rare and presents a unique clinical challenge. We report the case of an 8.5-year-old boy with MFS who developed precursor B-cell acute lymphoblastic leukemia with the ETV6-RUNX1 fusion gene. He achieved complete remission with initial chemotherapy. Two years later, he experienced a relapse involving the testes and central nervous system. Subsequent treatment led to severe complications. Whole exome sequencing revealed multiple pathogenic variants, including a CHEK2 mutation, potentially contributing to the malignancy and treatment-related toxicities. This case highlights the potential role of dysregulated transforming growth factor β signaling in MFS contributing to leukemogenesis. The patient’s severe complications and co-occurrence of MFS underscore the need for personalized therapeutic strategies and comprehensive, multidisciplinary care. Further research is essential to improve clinical outcomes.