Background The prevalence of smoking remains high in many low- and middle-income countries (LMICs), including the Southeast Asian nation of Cambodia. Smoking is especially hazardous for people with HIV. In Cambodia, approximately 43%-65% of men with HIV and 3%-5% of women with HIV smoke cigarettes. Thus, there is a critical need for cost-effective smoking cessation interventions for Cambodian people with HIV. This paper describes the design, methods, and data analysis plans for a randomized controlled trial assessing the efficacy of a theory-based mobile health smoking cessation intervention in Cambodian people with HIV. Objective This 2-group randomized controlled trial compares the efficacy of a mobile health–based automated messaging (AM) intervention versus standard care (SC) in facilitating smoking cessation among Cambodian people with HIV. Methods Cambodian people with HIV who currently smoke and are receiving antiretroviral treatment (target, N=800) will be randomized to (1) SC or (2) the AM intervention. SC participants will receive brief advice to quit smoking, written self-help materials, nicotine patches, and will complete weekly app-delivered dietary assessments for 26 weeks. AM participants will receive all SC components (but will complete smoking-related weekly assessments instead of dietary assessments), in addition to a fully automated tailored messaging program driven by the weekly assessments to facilitate smoking cessation. In the Phase-Based Model of smoking cessation, the cessation process is partitioned into 4 phases: motivation, preparation (precessation), cessation (quit date to 2 weeks post quit), and maintenance (up to 6 months post quit). Our AM program targets processes within these phases, including increasing motivation to quit, enhancing self-efficacy, obtaining social support, skills to cope with nicotine withdrawal symptoms and stress, and skills to maintain abstinence. All participants will complete baseline and 3-, 6-, and 12-month in-person follow-up assessments. The primary outcome is biochemically confirmed abstinence at 12 months, with 3- and 6-month abstinence as secondary outcomes. Potential mediators and moderators underlying treatment effects will be explored, and cost-effectiveness will be assessed. Results This study was approved by all relevant domestic and international institutional and ethical review boards. Participant recruitment commenced in January 2023. Data collection is expected to conclude by the end of 2025. Conclusions By demonstrating the greater efficacy and cost-effectiveness of AM relative to SC, this study has the potential to transform HIV care in Cambodia and prevent tobacco-related diseases. Furthermore, it may be adapted for use in other Cambodian populations and in other low- and middle-income countries. Ultimately, the AM approach to smoking cessation could greatly improve public health in the developing world and beyond. Trial Registration ClinicalTrials.gov NCT05746442; https://clinicaltrials.gov/ct2/show/NCT05746442 International Registered Report Identifier (IRRID) PRR1-10.2196/48923