Background: Pediatric emergency medicine (PEM) fellowships accept trainees who have completed a residency in either emergency medicine (EM) or pediatrics and have adopted 17 subcompetencies with accompanying set of milestones from these two residency programs. This study aims to examine the changes in milestone scores among common subcompetencies from the end of EM or pediatrics residency to early PEM fellowship and evaluates time to reattainment of scores for subcompetencies in which a decline was noted. Methods: This is a national, retrospective cohort study of trainees enrolled in PEM fellowship programs from July 2014 to June 2018. PEM fellowship program directors voluntarily submitted deidentified milestone reports within the study time frame, including end-of-residency reports. Descriptive analyses of milestone scores between end of residency and PEM fellowship were performed. Results: Forty-eight U.S. PEM fellowship programs (65%) provided fellowship milestone data on 638 fellows, 218 (34%) of whom also had end-of-residency milestone scores submitted. Of 218 fellows eligible for analysis, 210 (96%) had completed a pediatrics residency and eight (4%) had completed an EM residency. Pediatric-trained fellows had statistically significant decreases in mean milestone scores in all 10 shared subcompetencies. Reattainment of milestone scores across all common subcompetencies for both EM and pediatric-trained PEM fellows occurred by the end of fellowship. Conclusions: This study demonstrated declines in milestone scores from the end of primary residency training in pediatrics to early PEM fellowship in shared subcompetencies, which may suggest that performance expectations are reset at the beginning of PEM fellowship. Changes in subcompetency milestone anchors to provide subspecialty-specific context may be needed to more accurately define skills acquisition in the residency-to-fellowship transition.