Background People living with HIV often struggle with mental health comorbidities that lower their antiretroviral therapy (ART) adherence. There is growing evidence that depression treatment may improve ART adherence and result in improved HIV outcomes. Given that mental health services are severely underequipped in low-resource settings, including in Uganda, new solutions to increase access to mental health care and close the treatment gap are urgently needed. This protocol paper presents the Suubi-Mhealth study, which proposed to develop a mobile health (mHealth) intervention for use among Ugandan youths (14-17 years) with comorbid HIV and depression, taking into account their unique contextual, cultural, and developmental needs. Objective The proposed study is guided by the following objectives: (1) to develop and iteratively refine an intervention protocol for Suubi-Mhealth based on formative work to understand the needs of youths living with HIV; (2) to explore the feasibility and acceptability of Suubi-Mhealth on a small scale to inform subsequent refinement; (3) to test the preliminary impact of Suubi-Mhealth versus a waitlist control group on youths’ outcomes, including depression and treatment adherence; and (4) to examine barriers and facilitators for integrating Suubi-Mhealth into health care settings. Methods Youths will be eligible to participate in the study if they are (1) 14-17 years of age, (2) HIV-positive and aware of their status, (3) receiving care and ART from one of the participating clinics, and (4) living within a family. The study will be conducted in 2 phases. In phase 1, we will conduct focus group discussions with youths and health care providers, for feedback on the proposed intervention content and methods, and explore the feasibility and acceptability of the intervention. In phase II, we will pilot-test the preliminary impact of the intervention on reducing depression and improving ART adherence. Assessments will be conducted at baseline, 1-, 2-, and 6-months post intervention completion. Results Participant recruitment for phase 1 is completed. Youths and health care providers participated in focus group discussions to share their feedback on the proposed Suubi-Mhealth intervention content, methods, design, and format. Transcription and translation of focus group discussions have been completed. The team is currently developing Suubi-Mhealth content based on participants’ feedback. Conclusions This study will lay important groundwork for several initiatives at the intersection of digital therapeutics, HIV treatment, and mental health, especially among sub-Saharan African youths, as they transition through adolescence and into adult HIV care settings. Trial Registration ClinicalTrials.gov NCT05965245; https://clinicaltrials.gov/study/NCT05965245 International Registered Report Identifier (IRRID) DERR1-10.2196/54635