In summary, the present study aimed to understand associations between childhood trauma, genetic risk for Alzheimer’s disease via APOEε4, adolescent neural connectivity, and young adult AUD and PTSD. We found that there are sex- and trauma-specific associations between childhood trauma, APOEε4, and frontal alpha EEG coherence, and that those associations are also linked to differences in AUD and PTSD symptoms in young adulthood. These findings may be important for identifying individuals at greater risk for cognitive and psychiatric harms related to early childhood trauma and may also be used to inform neurophysiological treatments (e.g., transcranial magnetic stimulation) to reduce symptoms associated with traumatic stress. Future research that investigates mediating mechanisms (e.g., inflammation, epigenetics, alcohol initiation) and other genetic risk factors (e.g., polygenic scores for AD) would further expand understanding of links between trauma, genetics, neural connectivity and long-term psychiatric and brain health outcomes. Furthermore, studies that include richer phenotyping of trauma exposure, other influential adverse childhood experiences, and social determinants of health would better inform the degree to which trauma is associated with normative and atypical aging across the lifespan.