This study investigated mental health in schoolchildren in different living arrangements after parental separation. The study population included 31,519 children from the Danish National Birth Cohort, followed-up at age 11 in 2010-2014. Child mental health was measured with a maternal report of the Strength and Difficulties Questionnaire (SDQ). Associations between living arrangements and mental health were analyzed using logistic and linear regression models, taking into account early childhood indicators of the parents' relations, income, education and psychiatric care. At age 11, children living in a nuclear family had the lowest rate of total SDQ score, 8.9%. Of the children who had experienced parental separation, children in joint physical custody had the lowest adjusted odds ratio (OR)1.25 (95%-CI 1.09-1.44), for a high SDQ score relative to children living in a nuclear family, with adjusted ORs of 1.63 (1.42-1.86) and OR 1.72 (1.52-1.95) for sole physical custody arrangements with and without a new partner. An analysis of change in SDQ scores between ages 7 and 11 in children showed a similar pattern. This study indicates that joint physical custody is associated with slightly more favorable mental health in schoolchildren after parental separation than sole physical custody arrangements.