Objective To study the clinical features and prognostic impact of CRLF2 overexpression in children with B-cell acute lymphoblastic leukemia (B-ALL). Methods A retrospective study included pediatric B-ALL patients admitted to Sichuan Provincial Maternity and Child Health Care Hospital and Kunming Children's Hospital from October 2018 to October 2022. Patients were divided into a CRLF2 overexpression group and a control group without CRLF2 overexpression according to CRLF2 gene testing at initial diagnosis. Clinical features and prognosis between groups were compared. Results A total of 93 children with B-ALL were enrolled, including 29 with CRLF2 overexpression. The age of onset ranged from 2 to 12 years. At diagnosis, the proportions of hepatosplenomegaly and thrombocytopenia in the CRLF2 overexpression group were significantly lower than those in the control group (P<0.05), while the proportion of masses was significantly higher (P<0.05). Significantly higher CRLF2 protein expression in the CRLF2 overexpression group than in the control group (P<0.05). The mean 3-year event-free survival (EFS) and overall survival (OS) rates in the CRLF2 overexpression group were 75.9% and 85.9%, respectively, lower than the control group (90.1% and 91.0%, respectively), but the differences lacked statistical significance by log-rank test. Conclusions These findings suggest a potential role of CRLF2 overexpression in disease progression. Further studies with larger sample sizes are warranted to confirm its prognostic significance.