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Introduction Genomic testing allows for the identification of disease-causing genetic variants and may also reveal secondary findings (SF) unrelated to the reason for testing. As the list of medically actionable genes continues to grow, it is important to understand the impact of these findings on clinical care and patient experience, particularly in paediatric settings. This work will generate novel evidence on the clinical, patient, family and system impacts of medically actionable SF generated from genomic testing.Methods and analysis This mixed-methods, prospective, observational study will describe the impacts of SF on clinical care and the patient and family experience. Participants include probands and/or parents of probands who receive SF (ie, cases), clinicians involved in managing their care and controls matched 2:1 to cases based on age group, phenotype and primary genomic testing result. We aim to enrol 50 cases and 100 controls among those who receive genomic testing through Genome-wide Sequencing Ontario or other local sequencing initiatives in Ontario, Canada. Clinicians involved in follow-up care will complete questionnaires related to risk assessment, medical recommendations and clinical utility of SF post-result disclosure and one year later. Patient questionnaires will record health service use and psychological outcomes (ie, personal utility, empowerment) every 6 months for 2 years. These data will be compared between cases and controls using parametric tests. Cases will be invited to a qualitative interview to learn about their experiences. Data will be analysed using quantitative and qualitative techniques, triangulating datasets to enhance the validity and depth of the findings.Ethics and dissemination This study is approved by the Clinical Trials Ontario (CTO) Research Ethics Review System (REB# CTO 3655). We plan to present our results to academic, patient, clinician and decision-maker audiences through articles and presentations at provincial, national and international meetings.