Abstract Purpose This study was designed to determine whether the factor structure of the Post-Concussion Symptom Scale (PCSS) is consistent (i.e., invariant) in subgroups of youth with pre-existing attention-deficit/hyperactivity disorder (ADHD) or migraines. A four-factor model of the PCSS has empirical support (i.e., cognitive-sensory, sleep-arousal, vestibular-somatic, and affective symptoms), and the current investigation examined (i) whether this model is invariant across athletes with and without ADHD or migraines and (ii) group differences across symptom clusters. Methods Participants included a large sample of adolescent athletes (N=39,242; 54.4% boys; 13–18 years-old, M=15.50±1.27 years), among which 2,543 reported ADHD and 2,638 reported having migraines. The 22-item PCSS was administered at pre-season baseline. Statistical analyses included invariance testing across ADHD and migraine groups. Good fit was defined as CFI≥0.95. Effect sizes for group differences in symptom clusters were calculated. Results Configural invariance was established across participants with and without ADHD (CFI=0.967) and with and without migraines (CFI=0.965); however, weak invariance was not established for either diagnostic group. Effect sizes (Cohen’s d) of group differences varied by symptom cluster: cognitive-sensory (ADHD=0.44; migraine=0.38), sleep-arousal (0.33, 0.37), vestibular-somatic (0.17, 0.45), and affective (0.27, 0.28). Conclusion Although the four-factor model has been previously published and replicated among healthy student athletes, this model was only partially invariant for participants with ADHD or migraines. The cognitive-sensory factor showed the largest differences based on ADHD, whereas the vestibular-somatic factor showed the largest differences based on migraine history.