Abstract Objective This study examined associations between chronic physical health conditions (identified from hospital records) that are subject to school health care plans, and children’s emotional, behavioral, and social functioning during early (∼5 years of age) and middle childhood (∼11 years). Methods Participants were 21,304 Australian children from a representative longitudinal population cohort derived by multi-agency record linkage. Hospital presentations (admitted patients and emergency department) identified children with asthma (n = 1,573), allergies and anaphylaxis (n = 738), type 1 diabetes (n = 59), epilepsy (n = 87), and any of these conditions (n = 2,275), relative to 19,029 children without these presentations. Logistic regression analyses determined associations between these exposures and (i) emotional, behavioral, social, and overall vulnerabilities reported by teachers (early childhood) and children (middle childhood), and (ii) self-reported lack of sources of support (middle childhood). Results Prevalence of any condition in hospital records was 7.5% by early childhood, and 10.7% by middle childhood. Relative to peers without these presentations, small increases in risk of overall problems, and selected emotional, behavioral, and social problems, were apparent for children with any condition, and asthma specifically, in early and middle childhood. Large and pervasive effects were apparent for epilepsy, limited small effects in middle childhood only for allergies and anaphylaxis, and no increases in risk associated with type 1 diabetes examined in middle childhood. No condition was associated with increased risk of lacking supports. Conclusions Children with hospital records of chronic conditions, particularly epilepsy and asthma, might benefit from school-based care plans that integrate their physical and mental health support needs.