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Objective Children and young people (CYP) with special educational needs (SENs) have an increased risk of psychopathology and long-term physical conditions (LTCs) compared with their peers. Yet, exploring the overlap between SEN, psychopathology and physical health using population-based data is lacking. We explored this association in a large, nationally representative survey of school-age children aged 5–16 in England.Design A secondary analysis of the Mental Health of Children and Young People 2017 survey, applying multiple imputation and logistic regression models.Setting A nationally representative community-based sample of children in England.Patients 6673 children aged 5–16 years, with parent-reported data on SEN status, Education, Health and Care Plan (EHCP) status and LTCs, and clinically rated Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition (DSM-5) psychiatric diagnoses (via the Development and Well-being Assessment).Interventions None.Main outcome measures Parent-reported SEN status; EHCP statusResults Among CYPs with SEN (n=559), 73% (n=409) had a DSM-5 disorder and/or at least one LTC. CYP with psychiatric disorders or LTCs showed substantially higher odds of having SEN (adjusted OR (AOR) DSM-5=7.76, 95% CI 6.41 to 9.39; AOR LTC=2.76, 95% CI 2.31 to 3.29) compared with non-affected peers. The interaction between psychiatric disorder and male gender was significant, indicating stronger associations with SEN and EHCP for boys than for girls, whereas disorder-specific interactions were not significant.Conclusions For CYPs with SEN, comorbidity with psychopathology and LTC is common, which underscores the need for effective liaison between education, healthcare and social services to ensure comprehensive support for CYPs with complex needs.