Children with medical complexity (CMC) may be at a high risk of neurodevelopmental and mental health conditions given disease comorbidities and lived experiences. Little is known about the prevalence of these conditions at a population level. In this study, we estimated the prevalence of neurodevelopmental and mental health diagnoses in CMC relative to children without medical complexity and measured associations between these diagnoses in CMC and subsequent health care utilization and in-hospital mortality. We applied the Child and Adolescent Mental Health Disorders Classification System to identify neurodevelopmental and mental health diagnoses using all-payer claims data from three states (2012-2017). Poisson regression was used to compare outcomes in CMC with neurodevelopmental and mental health diagnoses to CMC without these diagnoses, adjusting for sociodemographic and clinical characteristics. Among 85 581 CMC, 39 065 (45.6%) had ≥1 neurodevelopmental diagnoses, and 31 703 (37.0%) had ≥1 mental health diagnoses, reflecting adjusted relative risks of 3.46 (3.42-3.50) for neurodevelopmental diagnoses and 2.22 (2.19-2.24) for mental health diagnoses compared with children without medical complexity. CMC with both neurodevelopmental and mental health diagnoses had 3.00 (95% confidence interval [CI]: 2.98-3.01) times the number of ambulatory visits, 69% more emergency department visits (rate ratio = 1.69, 95% CI: 1.66-1.72), 58% greater risk of hospitalization (rate ratio = 1.58, 95% CI: 1.50-1.67), and 2.32 times (95% CI: 2.28-2.36) the number of hospital days than CMC without these diagnoses. Neurodevelopmental and mental health diagnoses are prevalent among CMC and associated with increased health care utilization across the continuum of care. These findings illustrate the importance of recognizing and treating neurodevelopmental and mental health conditions in this population.