BACKGROUND: HIV incidence is growing most rapidly in the United States among young men who have sex with men (YMSM). Overwhelming evidence demonstrates that routine testing and expanded use of pre-exposure prophylaxis (PrEP) would dramatically reduce the population burden of HIV; however, uptake of both interventions is suboptimal among young adults. The use of mobile phone apps by YMSM is ubiquitous and may offer unique opportunities for public health interventions. MyChoices is a theory-driven app to increase HIV testing and PrEP uptake. It was developed by an interdisciplinary team based on feedback from a diverse sample of YMSM. OBJECTIVE: The aim of this paper is to describe the protocol for the refinement, beta testing, and pilot randomized controlled trial (RCT) to examine the acceptability and feasibility of the MyChoices app. METHODS: This 3-phase study includes 4 theater testing groups for app refinement with a total of approximately 30 YMSM; for beta testing, including quantitative assessments and exit interviews, with approximately 15 YMSM over a 2-month period; and for a pilot RCT with 60 YMSM. The pilot will assess feasibility, acceptability, and preliminary efficacy of the MyChoices app, compared with referrals only, in increasing HIV testing and PrEP uptake. All participants will be recruited at iTech clinical research sites in Boston, MA, and Bronx, NY. RESULTS: App refinement is underway. Enrollment for the pilot RCT began in October 2018. CONCLUSIONS: MyChoices is one of the first comprehensive, theory-driven HIV prevention apps designed specifically for YMSM. If MyChoices demonstrates acceptability and feasibility in this pilot RCT, a multicity, 3-arm randomized controlled efficacy trial of this app and another youth-optimized app (LYNX) versus standard of care is planned within iTech. If shown to be efficacious, the app will be scalable, with the ability to reach YMSM across the United States as well as be geographically individualized, with app content integrated with local prevention and testing activities. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/10694.