Recent meta-analyses have shown lower zinc and higher copper levels in the serum of people with schizophrenia than in healthy controls. However, the relationship between trace elements (TEs) and the pathophysiology of psychosis, including schizophrenia, remains unclear due to the antipsychotic effects on mineral levels. In this study, we aimed to determine the relationship between zinc and copper levels in hair and psychosis risk among drug-naïve adolescents. This study was conducted as a part of a population-based biomarker subsample study of the Tokyo Teen Cohort Study, including 252 community-dwelling 14-year-old drug-naïve adolescents. Zinc and copper levels in hair were measured using inductively coupled plasma mass spectrometry. The thought problems (TP) scale from the Child Behavior Checklist was used to evaluate psychosis risk. Regression analysis showed that hair zinc levels were negatively correlated with the TP scale (T-score) (β = −0.176, P = 0.005). This result remained significant after adjusting for age and sex (β = −0.175, P = 0.005). In contrast, hair copper levels were not associated with the TP scale (T-score) (β = 0.026, P = 0.687). These findings suggest that lower zinc levels could be involved in the pathophysiology of psychosis, independent of antipsychotics. Further longitudinal studies are required to investigate whether hair zinc level is a useful new biomarker for assessing psychosis risk.