BACKGROUND: Children and young people (CYP) with long-term physical conditions (LTCs) are more likely to have poorer mental health and more school absenteeism compared with CYP with no LTCs. However, there is limited longitudinal research, and the extent to which these difficulties persist in CYP with LTCs is unknown. Furthermore, little is known about the relative impact of different types of LTC on mental health and absenteeism. METHODS: We investigated cross-sectional and longitudinal associations of different LTCs with mental health and school absenteeism in a large (N = 7977) nationally representative survey of CYP in Great Britain and its 3-year follow-up. Psychopathology was assessed using the parent-reported Strengths and Difficulties Questionnaire (SDQ), and diagnosis of any psychiatric disorder using the Development and Wellbeing Assessment (DAWBA). Days absent and persistent absence (missing 10% or more of school days) were reported by parents. RESULTS: Compared with those with no LTCs, CYP with any LTC had higher SDQ total difficulties scores at baseline (adjusted mean difference 1.4, 1.1-1.6) and follow-up (1.1, 0.8-1.4) and were more likely to have a psychiatric disorder at baseline (adjusted odds ratio [aOR] 1.59, 1.34-1.89) and follow-up (1.75, 1.44-2.12). Children with any LTC also missed more days of school at baseline (adjusted incidence rate ratio 1.47, 1.31-1.64) and follow-up (1.17, 1.00-1.36) and were more likely to be persistently absent (aOR baseline 1.78, 1.48-2.14; follow-up 1.27, 1.00-1.61). Neurodevelopmental disorders, migraines and atopic conditions were particularly strongly associated with both mental health and absenteeism. CONCLUSIONS: Children with LTCs had poorer mental health and more school absence than those with no LTCs. Clinicians should routinely enquire about mental health and school attendance in CYP with LTCs and should collaborate with families and schools to ensure these children are provided with sufficient mental health and educational support.