We examined whether childhood cognitive ability was associated with two mental health outcomes at age 53 years: the 28 item General Health Questionnaire (GHQ-28) as a measure of internalising symptoms of anxiety and depression, and the CAGE screen for potential alcohol abuse as an externalising disorder. A total of 1875 participants were included from the Medical Research Council National Survey of Health and Development, also known as the British 1946 birth cohort. The results indicated that higher childhood cognitive ability was associated with reporting fewer symptoms of anxiety and depression GHQ-28 scores in women, and increased risk of potential alcohol abuse in both men and women. Results were adjusted for educational attainment, early socioeconomic status (SES) and adverse circumstances, and adult SES, adverse circumstances, and negative health behaviours. After adjusting for childhood cognitive ability, greater educational attainment was associated with reporting greater symptoms of anxiety and depression on the GHQ-28. Although undoubtedly interrelated, our evidence on the diverging effects of childhood cognitive ability and educational attainment on anxiety and depression in mid-adulthood highlights the need for the two to be considered independently. While higher childhood cognitive ability is associated with fewer internalising symptoms of anxiety and depression in women, it places both men and women at higher risk for potential alcohol abuse. Further research is needed to examine possible psychosocial mechanisms that may be associated with both higher childhood cognitive ability and greater risk for alcohol abuse. In addition, the underlying mechanisms responsible for the gender-specific link between childhood cognitive ability and the risk of experiencing internalising disorders in mid-adulthood warrants further consideration.