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Background The uptake of pre-exposure prophylaxis (PrEP) has been slow for young black men who have sex with men (BMSM) living in the southern United States. This is a significant issue because 8 of the 10 states with the highest rates of new HIV infections are in the South. Jackson, Mississippi (MS), the site of this project, has the second highest AIDS diagnosis rate in the nation and the highest rate of HIV infection for young, urban BMSM. This study will develop and test an engaging, interactive, and cost-effective mobile messaging intervention to improve engagement in PrEP care for BMSM aged 18 to 35 years living in Jackson, MS. Objective The goals of this mixed methods study are to (1) conduct qualitative interviews with young BMSM in Jackson, MS, to understand individual, community, and structural barriers affecting engagement in PrEP-related care, (2) assemble a PrEP mobile messaging intervention that includes text messages with publicly available internet content (websites and YouTube videos) that provide factual information, motivational materials, and behavioral skills related to PrEP and HIV prevention, and (3) evaluate the preliminary efficacy of the intervention in a randomized controlled study with PrEP-eligible BMSM receiving care in STI/HIV testing clinics in Jackson, MS. Methods This research protocol will be conducted in 2 phases. A development phase will involve in-depth interviews (n=30) with PrEP-eligible BMSM who receive care in STI/HIV testing clinics in MS. These interviews will allow researchers to select the texted material that will be sent out during the intervention. The second phase will consist of an unblinded, small, randomized controlled trial among 66 new participants to examine the preliminary efficacy of the intervention compared with enhanced standard of care (ESC) on attendance at a PrEP services appointment (the first step in initiating PrEP care) and receipt of a PrEP prescription, based on self-report and electronic medical records. The free, publicly available material will be sent to PrEP-eligible BMSM in 8 to 16 interactive text messages over 4 weeks. Study assessments will occur at enrollment and at 4- and 16-weeks postenrollment and can be completed online or in person. All participants will be recruited from a local clinic. Results Institutional review board approval was received on January 16, 2017, and research activities, subsequently, began in February 2018. Recruitment for the study concluded in November 2019. In total, 65 participants were randomized with 33 being assigned to the intervention and 32 to ESC. Collection of follow-up data is ongoing. Conclusions This PrEP mobile messaging intervention aims to increase uptake of PrEP by BMSM in the southern United States. This intervention uses interactive, tailored text messaging and appealing free Web content (publicly accessible educational websites and YouTube videos) to promote linkage to PrEP care and increase HIV preventative behaviors. A cost-effective PrEP mobile messaging intervention has great potential to improve information about PrEP, improve motivation to use PrEP, and decrease stigma and structural barriers that often prevent engagement in PrEP-related medical care. Trial Registration ClinicalTrials.gov NCT03308097; https://clinicaltrials.gov/ct2/show/NCT03308097 International Registered Report Identifier (IRRID) DERR1-10.2196/15781