In the current study, we seek to uncover neurodevelopmental patterns of brain connectivity in unaffected (with SCZ, BiP, or MDD) adolescents and young adults as a function of their polygenic susceptibility for SCZ. We also aim to understand important sex and developmental differences in these brain connectivity patterns. We examined associations between polygenic risk for SCZ32 and neurodevelopmental trajectories of EEG coherence throughout adolescence and young adulthood among unaffected (nonpsychotic) individuals. Data was drawn from the Collaborative Study on the Genetics of Alcoholism (COGA), with longitudinal data available throughout a key period of risk for the onset of psychotic illness, ages 12–32. We also examined sex-specific effects and developmental differences in the association of SCZ PRS and EEG coherence that may be otherwise masked. Finally, we examined whether PRS for genetically correlated neuropsychiatric conditions, BiP and MDD, were differentially associated with neurodevelopmental trajectories of connectivity.