Shift (Black Dog Institute) is the first mobile health smartphone appcreated to support the mental health of junior physicians. Junior physicians experience demanding work conditions, leading to high levels of psychological distress and burnout. However, they are often concerned about the potential career impacts of seeking mental health support. The confidentiality and ease of access of digital interventions may be particularly suited to address these concerns. The Shift app provides therapeutic and psychoeducational content and strategies contextualized for the specific needs of physicians in training. App content includes information on mental health, help seeking, mindfulness, and common workplace-related concerns of junior physicians. This study aims to test, at scale, the effectiveness of Shift among junior physicians working in Australia using a randomized controlled trial design. The primary aim is to examine whether junior physicians using Shift experience a reduction in depressive symptoms compared with a waitlist control group. The secondary aim is to examine whether the app intervention group experiences improvements in anxiety, work and social functioning, help seeking, quality of life, and burnout compared with the control group. A total of 778 junior physicians were recruited over the internet through government and nongovernment medical organizations across Australia, as well as through paid social media advertisements. They were randomly allocated to one of 2 groups: (1) the intervention group, who were asked to use the Shift app for a period of 30 days, or(2) the waitlist control group, who were placed on a waitlist and were asked to use the app after 3 months.Participants completed psychometric measures for self-assessing mental health and wellbeing outcomes, with assessments occurring at baseline, 1 month after completing the baseline period, and 3 months after completing the baseline period. Participants in the waitlist control group were asked to complete an additional web-based questionnaire 1 month after receiving access to the app or 4 months after completing the baseline survey. Participants took part in the study on the internet; the study was completely automated. The study was funded from November 2022 to December 2024 by the New South Wales Ministry of Health. Data collection for the study occurred between January and August 2024, with 780 participants enrolling in the study during this time. Data analysis is underway; the effectiveness of the intervention will be estimated on an intention-to-treat basis using a mixed-model, repeated measures analysis. Results are expected to be submitted for publication in 2025. To the best of our knowledge, this is the first randomized controlled trial to examine the effectiveness of a mobile health smartphone app specifically designed to support the mental health of junior physicians. Australia and New Zealand Clinical Trials Registry ACTRN12623000664640; https://tinyurl.com/7xt24dhk. DERR1-10.2196/58288.