BACKGROUND: Black and Hispanic women in the United States continue to bear disproportionate incidence of HIV related to sexual transmission and injection drug use. Specifically, women with substance use disorders (SUDs) are more likely to engage in vaginal or anal condomless sex associated with HIV transmission. Pre-exposure prophylaxis (PrEP) is a highly effective HIV prevention tool but is not widely used by racial or ethnic minority women. Effective interventions for engaging women with SUDs in HIV prevention interventions that are culturally appropriate and, therefore, more appealing to racial or ethnic minority women with SUDs are critically needed. OBJECTIVE: This 3-phased study, including a pilot randomized controlled trial (RCT), will assess the initial efficacy, feasibility, and acceptability of an addiction clinic-based behavioral and PrEP services intervention to increase the uptake and adherence to PrEP among racial or ethnic minority women. METHODS: A 3-phased mixed methods research design will involve formative qualitative methods using thematic analysis to design the intervention (phase 1), theatre testing to adapt and refine the intervention (phase 2), and RCT methods to pilot test the intervention for efficacy, feasibility, and acceptability (phase 3). The pilot RCT will enroll and randomize 60 women to either the standard SUD treatment program or SUD treatment integrated with PrEP services. The addiction clinic-based behavioral intervention will include 4 motivational counseling sessions guided by the Information-Motivation-Behavioral Skills Model to increase the uptake of PrEP. A mobile health app will be used to engage participants with the intention of motivating PrEP initiation and supporting adherence to PrEP. Following phase 3, generalized linear modeling will be used to model effects of the proportion of participants who fill their prescription and take at least 1 dose as a function of the intervention group. RESULTS: Findings from individual qualitative interviews informed the development of the addiction clinic-based behavioral intervention. Study recruitment for the randomized pilot (phase 3) launched in May 2024. Additional statistical analyses will be performed upon completion of the study. CONCLUSIONS: This addiction clinic-based behavioral intervention aims to increase PrEP uptake and adherence among racial or ethnic minority women who engage in sexual and substance use behaviors associated with increased susceptibility to HIV transmission. The addiction clinic-based behavioral intervention has the potential to reduce HIV-related disparities among Black and Hispanic women with SUDs. Findings from this study will provide a foundation for future HIV prevention interventions for racial or ethnic minority women with SUDs. TRIAL REGISTRATION: ClinicalTrials.gov NCT06158607; https://clinicaltrials.gov/study/NCT06158607?term=NCT06158607&rank=1. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/64961.