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Objective To determine the prevalence of significant motor difficulties at 12 years of age in children born extremely preterm (EPT, <28 weeks’ gestational age) compared with term-born peers and to identify associated risk factors and comorbidities.Design Population-based cohort study.Setting National cohort from the Extremely Preterm Infants in Sweden Study, including children born from 2004 to 2007.Patients Children born <27 weeks’ gestational age without cerebral palsy and/or severe neurodevelopmental impairment and term-born controls.Interventions Motor function was assessed at 12 years using the Movement Assessment Battery for Children, second edition (MABC-2). Logistic regression identified risk factors for motor difficulties.Main outcome measures Prevalence of significant motor difficulties, defined as scores ≤fifth percentile on MABC-2.Results A total of 268 EPT-born and 196 term-born children were assessed. Significant motor difficulties were found in 30% of EPT-born children compared with 3% of term-born peers (adjusted OR 16.99; 95% CI 6.64 to 43.47). Male sex and lower gestational age were independently associated with higher risk. Among EPT-born children with motor difficulties, comorbidities were common, including autism spectrum disorders and attention deficit hyperactivity disorders. Only 9.5% of affected children had received physiotherapy in the previous year.Conclusions Children born EPT, even in the absence of cerebral palsy and/or severe neurodevelopmental impairment, have a markedly increased risk of motor difficulties and associated neurodevelopmental comorbidities by age 12. Structured follow-up into mid-school age is essential to enable timely interventions.