Background: In pediatric B-cell precursor acute lymphoblastic leukemia (BCP-ALL), the IKZF1 gene deletions is an molecular marker of poor prognosis. We aimed to assess the prognostic effect of different levels of IKZF1 gene deletions in pediatric BCP-ALL. Procedure: IKZF1 Δ2-8/ALB deletions were quantified using multiplex real-time quantitative PCR (RQ-PCR) in newly diagnosed pediatric BCP-ALL patients between June 2014 and January 2018. Seventy-four patients with IKZF1 deletions of ≥ 0.01% were included. Clinical characteristics, laboratory data, and treatment outcomes were analyzed. Results: The patients were divided into two groups: IKZF1 deletions of < 1% (Group A) and of ≥ 1% (Group B). Patients in group B had a higher BCR-ABL1 positive rate than those in group A (P = 0.001). The proportions of patients who had an age at onset of ≥10 years old, and white blood cell count ≥ 50×109/L were significantly higher in group B than in group A (P < 0.05). The 3-year overall survival (OS) and 3-year event-free survival (EFS) rates in group B were 79 ± 8.8% and 62.4 ± 9.7%, respectively, which were significantly lower than the 3-year OS (97.7 ± 2.2%, P = 0.022) and 3-year EFS (83.2 ± 5.8%, P = 0.019) in group A. Multivariate analysis revealed that the level of IKZF1 deletions of ≥ 1% and CNSL were independent risk factors of EFS. Conclusions: Pediatric BCP-ALL patients with high levels of IKZF1 gene deletions have a poorer prognosis than those with low levels.