Abstract: Objective To investigate the incidence of the ETV6/RUNX1 fusion gene among Chinese pediatric patients with B-ALL and its effect on the prognosis. Methods A total of 723 patients with B-ALL from January 1, 2007 to December 31, 2014 were enrolled in this study. All patients were detected ETV6/RUNX1 fusion gene by FISH. Clinical data and ETV6/RUNX1 were combined to analyze the clinical prognosis. Results Among the 723 patients, 151 were with ETV6/RUNX1 positive B-ALL, accounting for approximately 20.89% (151/723) of B-precursor cases; 91 patients were with recurrence, including 10 patients with ETV6/RUNX1 positive B-ALL, and the recurrence rate of ETV6/RUNX1 positive B-ALL was 10.99% (10/91). Among 10 recurrent patients with ETV6/RUNX1 positive B-ALL, 9 patients relapsed more than 300 days later after diagnosis, while the recurrence times among the patients with ETV6/RUNX1 negative was very different. Although the recurrence times between the two groups showed no significant difference (P = 0.09), the recurrence times of ETV6/RUNX1 positive patients were mainly found at the end of clinical chemotherapy, while the recurrence time of ETV6/RUNX1 negative patients were mainly at maintaining chemotherapy period, there was a significant difference between the distribution of recurrence time (P < 0.0001). Conclusions ETV6/RUNX1 fusion gene is a favorable predictor of outcome in Chinese pediatric B-ALL as well.