Understanding individual variation in the continuity of youth mental health difficulties is critical for identifying the factors that promote recovery or chronicity. This study establishes the proportion of children showing psychopathology at 9 years, whose pathology had either remitted or persisted at 13. It describes the socio-demographic and clinical profiles of these groups, and examines the factors in 9-year-olds’ familial environments that predict longitudinal remission vs. persistence of psychopathology. The study utilised data from a prospective longitudinal study of 8568 Irish children. Child psychopathology was assessed using the Strengths and Difficulties Questionnaire (SDQ). Analysis established the rates of continuity of SDQ classifications between 9 and 13 years. Analysis also investigated the familial factors that predicted the remission vs. persistence of psychopathological symptoms, controlling for socio-demographic and child factors. Average SDQ scores improved between the ages of 9 and 13, F(1, 7292) = 276.52, p < 0.001, η2p = 0.04. Of children classified Abnormal aged 9, 41.1% remained so classified at 13, 21.4% were reclassified Borderline, and 37.6% Normal. Demographic and child risk factors for persistence of pathology were maleness (β = −1.00, p = 0.001, CI = 0.20–0.67), one-carer households (β = −0.71, p = 0.04, CI = 0.25–0.97), poor physical health (β = −0.64, p = 0.03, CI = 0.30–0.92), and low cognitive ability (β = 0.61, p = 0.002, CI = 1.26–2.70). Controlling for these factors, the only familial variable at 9 years that predicted subsequent pathological persistence was caregiver depression (β = −0.07, p = 0.03, CI = 0.87–0.99). The analysis highlights substantial rates of psychopathological discontinuity in a community sample and identifies the children most at risk of chronic mental health problems. These results will inform the targeting of early interventions and distribution of clinical resources.