ImportancePaediatric traumatic injury (PTI) is a leading cause of hospitalisation among children. Little is known about subsequent mental and physical health disorders while accounting for pre-injury health.ObjectiveTo compare pre-injury and post-injury mental and physical disorders in survivors of PTI with an uninjured matched cohort from the general population. This study hypothesised injured youth will have increased rates of mental and physical disorders relative to matched uninjured youth in the post-injury period.DesignRetrospective longitudinal cohort study using linked administrative health data to examine paediatric patients hospitalised for injury between 1 January 2004 and 31 December 2016, measured 2 years pre-injury and 2 years post-injury.SettingPopulation-based study in Manitoba, Canada.ParticipantsYouth<18 years old who survived to discharge after an injury requiring hospitalisation in the study period (n=9551) were matched 1:5 (age, sex and region) to youth from the general uninjured population (n=47 755).Exposure(s)PTI that required hospitalisation.Main outcomes and measuresMental disorders (anxiety, depression and substance use) and physical disorders (arthritis, cancer, diabetes, gastrointestinal, hypertension and total respiratory morbidity) were measured at physician visits and hospitalisations 2 years pre-injury and post-injury. Generalised estimating equations were used to estimate adjusted rate ratios (ARR).ResultsThis study examined 9551 in the injured cohort and 47 755 matches in the uninjured cohort. Injured individuals had increased ARRs for all mental disorders (p<0.0006) pre-injury (anxiety=1.30 (95% CI, 1.16 to 1.47); depression=2.00 (95% CI, 1.73 to 2.32); substance use=4.99 (95% CI, 3.08 to 5.20); any mental disorder=1.50 (95% CI, 1.37 to 1.66)) and post-injury (anxiety=1.66 (95% CI, 1.51 to 1.82); depression=2.87 (95% CI, 2.57 to 3.21); substance use=3.25 (95% CI, 2.64 to 3.99); any mental disorder=1.90 (95% CI, 1.76 to 2.04)). For physical disorders, injured individuals had increased ARRs (p<0.0006) pre-injury for arthritis (1.50 (95% CI, 1.39 to 1.60)), cancer (1.97 (95% CI, 1.35 to 2.88)), gastrointestinal (1.12 (95% CI, 1.06 to 1.18)) and any physical disorder (1.14 (95% CI, 1.11 to 1.18)). Post-injury, the injured had higher ARRs (p<0.0006) for arthritis (2.02 (95% CI, 1.91 to 2.15)), cancer (1.97 (95% CI, 1.35 to 2.88)), diabetes (1.76 (95% CI, 1.33 to 2.32)), gastrointestinal (1.19 (95% CI, 1.12 to 1.27)), hypertension (2.36 (95% CI, 1.83 to 3.06)) and any physical disorder (1.33 (95% CI, 1.29 to 1.37)). Comparing the pre-injury and post-injury periods, ARRs for injured showed a difference over time for all mental disorders except substance use and all physical disorders except gastrointestinal and total respiratory morbidity compared with matched uninjured. Greater injury severity was associated with two times greater ARR for developing any mental health disorder, and the injured had three times the ARR for dying by suicide (p<0.0006).Conclusions and relevanceChild survivors of traumatic injury had increased relative rates of mental and physical disorders compared with a matched uninjured cohort. These findings support targeted intervention strategies for this population at the time of hospitalisation.