This novel study explored associations between childhood trauma and longitudinal alpha EEG coherence in frontal brain regions in children and adolescents, and their association with subsequent AUD and PTSD in young adulthood. Our findings suggest that childhood assaultive trauma is associated with changes in neural connectivity patterns, and the nature of these associations differs by sex and trauma exposure type. Further, trajectories of neural connectivity were associated with subsequent AUD and PTSD symptoms. These findings contribute valuable insights into the neurodevelopmental consequences of childhood trauma, extending beyond the predominantly cross-sectional adult literature. Importantly, sex-specific variations in neural connectivity underscore the need for a comprehensive understanding of trauma's impact on brain functioning. The relevance of EEG coherence as a potential biomarker for early diagnosis and targeted interventions is also emphasized. Moving forward, integrating machine learning techniques and exploring other genetic and biological factors could enhance our understanding of the shared neurobiological mechanisms underlying PTSD, AUD, and trauma-related EEG coherence, with the goal to guide targeted interventions for high-risk groups.