Background Timely and comprehensive treatment in the form of early psychosis intervention (EPI) has become the standard of care for youth with psychosis. While EPI services were designed to be delivered in person, the COVID-19 pandemic required many EPI programs to rapidly transition to virtual delivery, with little evidence to guide intervention adaptations or to support the effectiveness and satisfaction with virtual EPI services. Objective This study aims to explore the adaptations required to deliver NAVIGATE, a model of coordinated specialty care used in EPI, in a virtual format. This study will evaluate implementation of the NAVIGATE model delivered virtually by describing the nature of the adaptations to the intervention, assessing fidelity to the EPI model and the satisfaction of clients, family members, and care providers. We will investigate barriers and facilitators to virtual NAVIGATE implementation, service engagement, and health equity impacts of this work. Methods The Centre for Addiction and Mental Health (Toronto, Ontario, Canada) transitioned to delivering NAVIGATE virtually early in the COVID-19 pandemic. The Framework for Reporting Adaptations and Modifications for Evidence-Based Interventions will be used to describe the adaptations required to deliver NAVIGATE virtually. Fidelity to the EPI model will be measured using the First Episode Psychosis Services Fidelity Scale and fidelity to NAVIGATE will be assessed by investigating adherence to its core components. Implementation facilitators and barriers will be explored using semistructured interviews with providers informed by the Consolidated Framework for Implementation Research. Satisfaction with virtually delivered NAVIGATE will be assessed with virtual client and provider experience surveys and qualitative interviews with clients, family members, and providers. Service engagement data will be collected through review of medical records, and potential impacts of virtually delivered NAVIGATE on different population groups will be assessed with the Health Equity Impact Assessment. Results Virtual clinical delivery of NAVIGATE started in March 2020 with additional adaptations and data collection is ongoing. Data will be analyzed using descriptive statistics and survival analysis for quantitative data. Qualitative data will be analyzed using thematic content analysis. Integration of qualitative and quantitative data will occur at the data collection, interpretation, and reporting levels following a convergent design. Conclusions This study will provide information regarding the type of intervention adaptations required for virtual delivery of NAVIGATE for youth with early psychosis, ensuring access to high-quality care for this population during the pandemic and beyond by guiding future implementation in similar contexts. International Registered Report Identifier (IRRID) DERR1-10.2196/34591