BACKGROUND: While access to pre-exposure prophylaxis (PrEP) is an important tool for reducing HIV incidence in the United States, disparities in uptake by race, sex, socioeconomic status, and geography persist. In 2018, the US South accounted for more than half of all new HIV diagnoses but only one-third of PrEP users. PrEP use in North Carolina (NC) similarly lags, with uptake being the lowest among young, sexual and gender minority populations, who account for nearly two-thirds of the state's incident infections. The PrEP-to-need ratio, a metric of PrEP equity that measures PrEP uptake relative to new HIV diagnoses, highlights disparities in PrEP uptake among specific demographic groups such as women and Black, Hispanic, and Southern people, indicating that these groups are underserved relative to their epidemic need. Despite behavioral risk overlap of incident sexually transmitted infections (STIs) and HIV, in NC, PrEP is only offered at a few primarily urban health department-affiliated STI clinics. The lack of robust health care infrastructure in these areas presents challenges for HIV prevention services. OBJECTIVE: This protocol describes a randomized controlled trial of a multilevel PrEP intervention recruiting from rural and periurban STI clinics. METHODS: This trial aims to enroll up to 336 participants and randomly assign them 1:1 to either the intervention or control group. The intervention consists of access to a digital health app, linkage to a remote PrEP navigator, and the option of referral to telehealth-based PrEP services. Persons randomly assigned to the control condition will receive an enhanced standard of care, including access to a limited version of the digital health app. All participants will be followed up on quarterly for at least 3 months. The primary outcome is the initiation of PrEP within 3 months of an index STI clinic visit; secondary outcomes evaluate PrEP care engagement and adherence, incident HIV and bacterial STI infections, PrEP stigma, and cost-effectiveness. Binary outcome analyses will estimate the proportion of participants achieving an event (eg, PrEP uptake) in each arm and a probability difference and the corresponding 95% CI to compare the intervention versus control arm at each time point. Continuous end points will use nonparametric Wilcoxon rank sum tests comparing the intervention and control groups. RESULTS: Enrollment opened on August 31, 2023, at 15 health departments in NC and subsequently expanded to 21 facilities in 20 counties by July 2024. Completion of the enrollment and data collection phases is expected by May 2025. Results will be published thereafter. CONCLUSIONS: This study directly addresses multiple barriers to PrEP use in rural and periurban areas of the Southeastern United States and can inform policy and programming that seek to expand PrEP access and promote use in underserved communities. TRIAL REGISTRATION: ClinicalTrials.gov NCT05984030; https://clinicaltrials.gov/study/NCT05984030. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/68085.