Changes in pain scores that represent clinically significant differences in children with headaches are necessary for study design and interpretation of findings reported in studies. We aimed to determine changes in pain scores associated with a minimum clinically significant difference (MCSD), ideal clinically significant difference (ICSD), and patient-perceived adequate analgesia (PPAA) in this population. We performed a secondary analysis of two prospective studies of children with headaches presenting to an emergency department. Two serial assessments were performed in children aged 6-17 and 4-17 years who self-reported their pain intensity using the Verbal Numerical Rating Scale (VNRS) and Faces Pain Scale-Revised (FPS-R), respectively. Children qualitatively described any endorsed change in pain score; those who received an analgesic were asked if they wanted additional analgesics to decrease their pain intensity. We used receiver operating characteristic curve-based methodology to identify changes in pain scores associated with "a little less" (MCSD) and "much less" (ICSD) pain and patients declining additional analgesics because they experienced adequate analgesia after treatment (PPAA). We analyzed 105 children: 63.8% were female and the median (IQR) age was 13 (10-15) years. Ninety-eight children were analyzed for the VNRS and 101 were analyzed for the FPS-R. For the VNRS, raw change and percent reductions in pain scores associated with MCSD, ICSD, and PPAA were 2/10 and 25%, 4/10 and 56%, and 3/10 and 50%, respectively, and for the FPS-R, 2/10 and 25%, 4/10 and 67%, and 4/10 and 60%, respectively. The area under the curve (AUC) associated with a MCSD for both scales ranged from 94% to 98%; the AUC associated with an ICSD or PPAA for both scales ranged from 76% to 83%. We identified changes in pain score associated with patient-centered outcomes in children with headaches suitable for designing trials and assigning clinical significance to changes in pain scores reported in studies.