Maternal thyroid problems during pregnancy have been linked to neurocognitive impairments in children. While studies suggest that disorders of maternal thyroid function during pregnancy are associated with symptoms of mental health problems in children, little is known about the risk of clinically significant psychiatric disorders in adolescence. A sample of 2451 Canadian adolescents enrolled in the Ontario Child Health Study completed the Mini International Neuropsychiatric Interview for Children and Adolescents at 12–17 years of age. Their mothers self-reported thyroid problems during pregnancy. Gestational thyroid problems were associated with offspring oppositional defiant disorder (ODD; OR 3.73; 95% CI 1.69–8.24), conduct disorder (CD; OR 12.95; 95% CI 5.12–32.75), and social anxiety disorder (SAD; OR 6.25; 95% CI 2.53–15.47). Neither sex nor gestational age moderated associations between prenatal thyroid dysfunction and the majority of outcomes. School performance mediated 8% of the association between thyroid problems and SAD, 21% for CD and 53% for ODD.