Abstract Background Young people account for more than a quarter of new HIV infections in the US, with the majority of cases among young men who have sex with men; young transgender women are also vulnerable to infection. Substance use, particularly alcohol misuse, is a driver of sexual transmission and a potential barrier to engagement in the HIV prevention and care continuum, however vulnerable youth are difficult to reach for substance use services due, in part, to complex social and structural factors and limited access to health care. The Community Prevention Services Task Force recommends electronic screening and brief intervention as an evidence-based intervention for the prevention of excessive alcohol consumption; however, no prior studies have extended this model to community-based populations of youth that are susceptible to HIV infection. This paper describes the study protocol for an electronic screening and brief intervention to reduce alcohol misuse among adolescents and young adults vulnerable to HIV infection in community-based settings. Methods This study, Step Up, Test Up, is a randomized controlled trial of an electronic alcohol screening and brief intervention among youth, ages 16–25, who are vulnerable to HIV infection. Individuals who present for HIV testing at one of three community-based locations are recruited for study participation. Eligibility includes those aged 16–25 years, HIV-negative or unknown HIV status, male or trans female with a history of sex with men, and English-speaking. Participants who screen at moderate to high risk for alcohol misuse on the Alcohol Use Disorders Identification Test (AUDIT) are randomized (1:1) to either an electronic brief intervention to reduce alcohol misuse or a time-and attention-matched control. The primary outcome is change in the frequency/quantity of recent alcohol use at 1, 3, 6 and 12-month follow-up. Discussion Testing of evidence-based interventions to reduce alcohol misuse among youth vulnerable to HIV infection are needed. This study will provide evidence to determine feasibility and efficacy of a brief electronically-delivered intervention to reduce alcohol misuse for this population. Trial registration ClinicalTrials.gov number, NCT02703116, registered March 9, 2016.