BackgroundIn Cambodia, HIV prevalence is concentrated in key populations including among female entertainment workers (FEWs) who may engage in direct or indirect sex work. Reaching FEWs with sexual and reproductive health (SRH) services has been difficult because of their hidden and stigmatized nature. Mobile-phone-based interventions may be an effective way to reach this population and connect them with the existing services. This article describes study design and implementation of a randomized controlled trial (RCT) of a mobile health intervention (the Mobile Link) aiming to improve SRH and related outcomes among FEWs in Cambodia.MethodsA two-arm RCT will be used to determine the effectiveness of a mobile-phone-based text/voice messaging intervention. The intervention will be developed through a participatory process. Focus group discussions and in-depth interviews have been conducted to inform and tailor behavior change theory-based text and voice messages. During the implementation phase, 600 FEWs will be recruited and randomly assigned into one of the two arms: (1) a control group and (2) a mobile phone message group (either text messages [SMS] or voice messages [VM], a delivery method chosen by participants). Participants in the control group will also receive a weekly monitoring survey, which will provide real-time information to implementing partners to streamline outreach efforts and be able to quickly identify geographic trends. The primary outcome measures will include self-reported HIV and sexually transmitted infections (STI) testing and treatment, condom use, contraceptive use, and gender-based violence (GBV).DiscussionIf the Mobile Link trial is successful, participants will report an increase in condom use, linkages to screening and treatment for HIV and STI, and contraception use as well as a reduction in GBV. This trial is unique in a number of ways. First, the option of participation mode (SMS or VM) allows participants to choose the message medium that best links them to services. Second, this is the first RCT of a mobile-phone-based behavior change intervention using SMS/VMs to support linkage to SRH services in Cambodia. Lastly, we are working with a hidden, hard-to-reach, and dynamic population with which existing methods of outreach have not been fully successful.Trial registrationClinical trials.gov, NCT03117842. Registered on 31 March 2017.Electronic supplementary materialThe online version of this article (10.1186/s13063-018-2614-7) contains supplementary material, which is available to authorized users.