Background The continual increase in patient attendance at the emergency department (ED) is a worldwide health issue. The aim of this study was to determine whether the use of a secondary prioritization software reduces the patients’ median length of stay (LOS) in the pediatric ED. Methods A randomized, controlled, open-label trial was conducted over a 30-day period between March 15th and April 23rd 2021 at Lille University Hospital. Work days were randomized to use the patient prioritization software or the pediatric ED’s standard dashboard. All time intervals between admission and discharge were recorded prospectively by a physician not involved in patient care during the study period. The study’s primary endpoint was the LOS in the pediatric ED, which was expected to be 15 min shorter in the intervention group than in the control group. The secondary endpoints were specific time intervals during the stay in the pediatric ED and levels of staff satisfaction. Results 1599 patients were included: 798 in the intervention group and 801 in the control group. The median [interquartile range] LOS was 172 min [113–255] in the intervention group and 167 min [108–254) in the control group (p = 0.46). In the intervention group, the time interval between admission to the first medical evaluation for high-priority patients and the time interval between the senior physician’s final evaluation and patient discharge were shorter (p < 0.01). The median satisfaction score was 68 [55–80] (average). Conclusion The patients’ total LOS was not significantly shorter on days of intervention. However, use of the electronic patient prioritization tool was associated with significant decreases in some important time intervals during care in the pediatric ED.