Background: The rates of physical inactivity and related cancer incidence and mortality are disproportionately high in the Deep South region in the United States, a rural, medically underserved region with a large African American population compared with the rest of the nation. Given this region's lower rates of literacy and internet access, interactive voice response (IVR) system-automated telephone-based interventions have the potential to help overcome physical activity intervention barriers (literacy, internet access, costs, and transportation) but have yet to be extended to rural, underserved populations, such as in the Deep South. Thus, extensive formative research is being conducted to develop and beta test the Deep South IVR System-Supported Active Lifestyle intervention in preparation for dissemination in rural Alabama counties. Objective: This paper aims to describe the design and rationale of an ongoing efficacy trial of the Deep South IVR System-Supported Active Lifestyle intervention. Methods: A two-arm randomized controlled trial will be conducted to compare a 12-month physical activity intervention versus a wait-list control condition in 240 underactive adults from 6 rural Alabama counties. The Deep South IVR System-Supported Active Lifestyle intervention is based on the Social Cognitive Theory and includes IVR-automated physical activity-related phone counseling (daily in months 0-3, twice weekly in months 4-6, and weekly in months 7-12) and support from local rural county coordinators with the University of Alabama O'Neal Comprehensive Cancer Center Community Outreach and Engagement Office. The primary outcome is weekly minutes of moderate- to vigorous-intensity physical activity (7-day physical activity recall; accelerometry) at baseline, 6 months, 12 months, and 18 months. Rural Active Living Assessments will be conducted in each rural county to assess walkability, assess recreational amenities, and inform future environment and policy efforts. Results: This study was funded in March 2019 and approved by the institutional review board of the University of Alabama at Birmingham in April 2019. As of February 2020, start-up activities (hiring and training staff and purchasing supplies) were completed. Study recruitment and assessments began in September 2020 and are ongoing. As of February 2021, a total of 43 participants have been enrolled in Dallas County, 42 in Sumter County, and 51 in Greene County. Conclusions: IVR-supported phone counseling has great potential for addressing physical activity barriers (eg, culture, literacy, cost, or transportation) and reducing related rural health disparities in this region.