BACKGROUND: New HIV infections occur at a disproportionately high rate among young men who have sex with men (YMSM). It is, therefore, essential that comprehensive HIV prevention strategies, specifically tailored to their needs and perceptions, are developed, tested, and disseminated. Antiretroviral pre-exposure prophylaxis (PrEP) is effective in decreasing HIV transmission among men who have sex with men; however, adherence is critical to its efficacy. In open-label studies among YMSM, adherence was suboptimal. Hence, behavioral approaches that address the unique challenges to YMSM PrEP adherence are needed. OBJECTIVE: This study aims to describe the protocol for intervention refinement and a pilot randomized controlled trial (RCT) of a PrEP adherence intervention, LifeSteps for pre-exposure prophylaxis for young men who have sex with men (LSPY). METHODS: This study includes the following 2 phases: formative qualitative interviews with approximately 20 YMSM and 10 key informants for intervention adaptation and refinement and a pilot RCT of up to 50 YMSM to assess the feasibility, acceptability, and preliminary efficacy of the LSPY, compared with the PrEP standard of care, to improve PrEP adherence. Participants will be recruited at 3 iTech subject recruitment venues in the United States. RESULTS: Phase 1 is expected to begin in June 2018, and enrollment of phase 2 is anticipated to begin in early 2019. CONCLUSIONS: Few rigorously developed and tested interventions have been designed to increase PrEP adherence among YMSM in community settings, despite this population's high HIV incidence. The long-term goal of this intervention is to develop scalable protocols to optimize at-risk YMSM's PrEP uptake and adherence to decrease the HIV incidence. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/10661.