Objective To study the association between S100A8 expression and prognosis in children with acute lymphoblastic leukemia (ALL). Methods The clinical data of 377 children with ALL who were treated with the CCLG-2008-ALL regimen were retrospectively reviewed. ELISA and PCR were used to measure serum protein levels and mRNA expression of S100A8. The Kaplan-Meier method was used for survival analysis and a Cox regression analysis was also performed. Results The children were followed up for 56 months, and the overall survival rate of the 377 children was 89.1%. The prednisone good response group had significantly lower S100A8 protein and mRNA levels than the prednisone poor response group (P < 0.01). In the children with standard or median risk, both S100A8 protein and mRNA levels were associated with event-free survival rate (P < 0.05). There were significant differences in S100A8 protein and mRNA levels between the children with different risk stratifications (P < 0.01). The children who experienced events had significantly higher S100A8 protein and mRNA levels than those who did not (P < 0.01). The Kaplan-Meier survival analysis and the Cox regression model suggested that S100A8 overexpression was an independent risk factor for the prognosis of children with ALL. Conclusions High S100A8 expression may be associated with the poor prognosis of children with ALL and is promising as a new marker for individualized precise treatment of children with ALL.