Background: Understanding gender gaps in trainee evaluations is critical because these may ultimately determine the duration of training. Currently, no studies describe the influence of gender on the evaluation of pediatric emergency medicine (PEM) fellows. Objective: The objective of our study was to compare milestone scores of female versus male PEM fellows. Methods: This is a multicenter retrospective cohort study of a national sample of PEM fellows from July 2014 to June 2018. Accreditation Council for Medical Education (ACGME) subcompetencies are scored on a 5-point scale and span six domains: patient care (PC), medical knowledge, systems-based practice, practice-based learning and improvement, professionalism, and interpersonal and communication skills (ICS). Summative assessments of the 23 PEM subcompetencies are assigned by each program’s clinical competency committee and submitted semiannually for each fellow. Program directors voluntarily provided deidentified ACGME milestone reports. Demographics including sex, program region, and type of residency were collected. Descriptive analysis of milestones was performed for each year of fellowship. Multivariate analyses evaluated the difference in scores by sex for each of the subcompetencies. Results: Forty-eight geographically diverse programs participated, yielding data for 639 fellows (66% of all PEM fellows nationally); sex was recorded for 604 fellows, of whom 67% were female. When comparing the mean milestone scores in each of the six domains, there were no differences by sex in any year of training. When comparing scores within each of the 23 subcompetencies and correcting the significance level for comparison of multiple milestones, the scores for PC3 and ICS2 were significantly, albeit not meaningfully, higher for females. Conclusion: In a national sample of PEM fellows, we found no major differences in milestone scores between females and males.