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The relative difference of resting EEG frontal alpha activation between left and right hemispheres (FAA; i.e., asymmetry) correlates with global approach and avoidance tendencies. FAA may relate to problems with executive and affective functioning in children with neurodevelopmental differences, including autism and ADHD. We (1) characterize relative left vs. right FAA in autistic, ADHD, and neurotypical children (NT) and (2) investigate whether FAA predicts “hot” executive function or emotion dysregulation. Participants were 97 7- to 11-year-old autistic, ADHD, and NT Children. Children with ADHD displayed greater left (relative to right) FAA compared to autistic and neurotypical children. Children with ADHD displayed greater challenges with “hot” EF on a gambling task than autistic children, whereas children with co-occurring autism and ADHD had greater parent-reported emotion dysregulation than NT and autism-only groups. Greater left FAA predicted worse hot EF for all children but was not significantly related to emotion dysregulation. Regardless of clinical diagnosis, relatively greater left FAA relates to hot EF. While hot EF deficits may be specific to ADHD rather than autism, both together confer additive risk for emotion dysregulation. Future research should explore the functional relation between FAA, reward processing, and affect for children with different EF-related neurodevelopmental differences.