Background: Pediatric emergency medicine (PEM) fellowships recruit trainees from both pediatric and emergency medicine (EM) residencies. The Accreditation Council for Graduate Medical Education (ACGME) defines separate training pathways for each. The 2015 PEM milestones reflect a combination of subcompetencies from the two residencies. This project aims to compare the milestone achievement of PEM fellows based on their primary residency training. We hypothesize that fellows trained in pediatrics achieve PEM milestones at different rates than EM-trained fellows in the ACGME domains of patient care, medical knowledge, systems-based practice, practice-based learning, professionalism, and interpersonal and communication skills. Methods: This is a multicenter, retrospective cohort study of fellows from a national sample of U.S. PEM fellowship programs. Basic demographic information and deidentified, biannual milestone scores for 23 competencies were collected for fellows training between 2015 and 2018. Subcompetencies are scored on a 5-point milestone scale. Descriptive and multivariable analyses for longitudinal data were performed to compare milestone assessments by primary residency training. Results: Complete data were obtained for 600 fellows; 95% (570) and 5% (30) completed pediatric and EM residency, respectively. In both year 1 and year 2 of fellowship, the mean milestone scores of EM-trained fellows were statistically higher than pediatrics-trained fellows across the majority of subcompetencies. By the final year of training, there were no statistically significant differences in milestone scores for any of the subcompetencies. Conclusions: Fellow milestone achievement between groups was not significantly different by graduation. However, fellows entering PEM training from an EM background attained higher scores on the milestones than fellows from a pediatric background in the first year of fellowship.