Electronic health record (EHR)-integrated digital personal health records (PHRs) via Fast Healthcare Interoperability Resources (FHIR) are promising digital health tools to support care coordination (CC) for children and youth with special health care needs but remain widely unadopted; as their adoption grows, mixed methods and implementation research could guide real-world implementation and evaluation. This study (1) evaluates the feasibility of an FHIR-enabled digital PHR app for CC for children and youth with special health care needs, (2) characterizes determinants of implementation, and (3) explores associations between adoption and patient- or family-reported outcomes. This nonrandomized, single-arm, prospective feasibility trial will test an FHIR-enabled digital PHR app's use among families of children and youth with special health care needs in primary care settings. Key app features are FHIR-enabled access to structured data from the child's medical record, families' abilities to longitudinally track patient- or family-centered care goals, and sharing progress toward care goals with the child's primary care provider via a clinician dashboard. We shall enroll 40 parents or caregivers of children and youth with special health care needs to use the app for 6 months. Inclusion criteria for children and youth with special health care needs are age 0-16 years; primary care at a participating site; complex needs benefiting from CC; high hospitalization risk in the next 6 months; English speaking; having requisite technology at home (internet access, Apple iOS mobile device); and an active web-based EHR patient portal account to which a parent or caregiver has full proxy access. Digital prescriptions will be used to disseminate study recruitment materials directly to eligible participants via their existing EHR patient portal accounts. We will apply an intervention mixed methods design to link quantitative and qualitative (semistructured interviews and family engagement panels with parents of children and youth with special health care needs) data and characterize implementation determinants. Two CC frameworks (Pediatric Care Coordination Framework; Patient-Centered Medical Home) and 2 evaluation frameworks (Consolidated Framework for Implementation Research; Technology Acceptance Model) provide theoretical foundations for this study. Participant recruitment began in fall 2022, before which we identified >300 potentially eligible patients in EHR data. A family engagement panel in fall 2021 generated formative feedback from family partners. Integrated analysis of pretrial quantitative and qualitative data informed family-centered enhancements to study procedures. Our findings will inform how to integrate an FHIR-enabled digital PHR app for children and youth with special health care needs into clinical care. Mixed methods and implementation research will help strengthen implementation in diverse clinical settings. The study is positioned to advance knowledge of how to use digital health innovations for improving care and outcomes for children and youth with special health care needs and their families. ClinicalTrials.gov NCT05513235; https://clinicaltrials.gov/study/NCT05513235. DERR1-10.2196/46847.