BACKGROUND: Transitional-aged youth have a high burden of mental health difficulties in Canada, with Indigenous youth, in particular, experiencing additional circumstances that challenge their well-being. Mobile health (mHealth) approaches hold promise for supporting individuals in areas with less access to services such as Northern Ontario. OBJECTIVE: The primary objective of this study is to evaluate the effectiveness of the JoyPop app in increasing emotion regulation skills for Indigenous transitional-aged youth (aged 18-25 years) on a waitlist for mental health services when compared with usual practice (UP). The secondary objectives are to (1) evaluate the impact of the app on general mental health symptoms and treatment readiness and (2) evaluate whether using the app is associated with a reduction in the use (and therefore cost) of other services while one is waiting for mental health services. METHODS: The study is a pragmatic, parallel-arm randomized controlled superiority trial design spanning a 4-week period. All participants will receive UP, which involves waitlist monitoring practices at the study site, which includes regular check-in phone calls to obtain any updates regarding functioning. Participants will be allocated to the intervention (JoyPop+UP) or control (UP) condition in a 1:1 ratio using stratified block randomization. Participants will complete self-report measures of emotion regulation (primary outcome), mental health, treatment readiness, and service use during 3 assessments (baseline, second [after 2 weeks], and third [after 4 weeks]). Descriptive statistics pertaining to baseline variables and app usage will be reported. Linear mixed modeling will be used to analyze change in outcomes over time as a function of condition assignment, while a cost-consequence analysis will be used to evaluate the association between app use and service use. RESULTS: Recruitment began September 1, 2023, and is ongoing. In total, 2 participants have completed the study. CONCLUSIONS: This study will assess whether the JoyPop app is effective for Indigenous transitional-aged youth on a waitlist for mental health services. Positive findings may support the integration of the app into mental health services as a waitlist management tool. TRIAL REGISTRATION: ClinicalTrials.gov NCT05991154; https://clinicaltrials.gov/study/NCT05991154. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/64745.