Background Adolescence hosts a sharp increase in the incidence of mental disorders. The prodromal phases are often characterized by cognitive deficits that predate disease onset by several years. Characterization of cognitive performance in relation to normative trajectories may have value for early risk assessment and monitoring. Methods Youth aged 8 to 21 years (N = 6481) from the Philadelphia Neurodevelopmental Cohort were included. Performance scores from a computerized neurocognitive battery were decomposed using principal component analysis, yielding a general cognitive score. Items reflecting various aspects of psychopathology from self-report questionnaires and collateral caregiver information were decomposed using independent component analysis, providing individual domain scores. Using normative modeling and Bayesian statistics, we estimated normative trajectories of cognitive function and tested for associations between cognitive deviance and psychopathological domain scores. In addition, we tested for associations with polygenic scores for mental and behavioral disorders often involving cognition, including schizophrenia, bipolar disorder, attention-deficit/hyperactivity disorder, and Alzheimer’s disease. Results More negative normative cognitive deviations were associated with higher general psychopathology burden and domains reflecting positive and prodromal psychosis, attention problems, norm-violating behavior, and anxiety. In addition, better performance was associated with higher joint burden of depression, suicidal ideation, and negative psychosis symptoms. The analyses revealed no evidence for associations with polygenic scores. Conclusions Our results show that cognitive performance is associated with general and specific domains of psychopathology in youth. These findings support the close links between cognition and psychopathology in youth and highlight the potential of normative modeling for early risk assessment.