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Children and youth with special health care needs (CYSHCN) have a range of medical, educational, and support service needs to achieve optimal health and wellness. Principles of care for CYSHCN have been well described, but the literature is lacking particularly on implementation and integration of care across different settings and systems. The objective of this manuscript is to define a research agenda for principles of care for CYSHCN.Literature review examined principles of care for CYSHCN. Existing research gaps and priorities for principles of care were drawn from the literature review, a recently developed national research agenda for CYSHCN, and stakeholder consensus.Specific implementation areas of inquiry include family partner roles within and across systems; life course approach for CYSHCN; roles and training of interdisciplinary team members; and implementation, spread, and sustainability studies. Proposed methods include implementation science-based and comparative effectiveness research. A common set of metrics including health care utilization, clinical outcomes, and family and provider needs should be considered to evaluate implementation of principles of care.Implementation science and comparative effectiveness methods are needed to further understanding about how to adopt and spread principles of care for CYSHCN. The evolving demographics of CYSHCN add relevance and urgency for research findings.