IntroductionSexually transmitted infections (STIs) are a significant public health concern globally, particularly affecting young women. Early diagnosis and treatment are essential to reducing or stopping the continuous spread of infections and the development of the associated complications. Syndromic management, which is commonly used for STIs, presents several barriers, particularly for young women. This protocol is for a study that aims to understand young women’s preferences for a self-sampling intervention for STI diagnosis by using a Discrete Choice Experiment (DCE).Methods and analysisThe following attributes of a self-sampling intervention were identified through a Nominal Group Technique: accessibility, education, confidentiality, self-sampling method, youth-friendliness, and cost. A pilot study involving 20 participants was conducted to refine the DCE questionnaire. A total of 196 young women from underserved communities will be recruited. The participants will be sampled from communities, stratified by settlement type and socioeconomic status. Data will be analysed using the multinomial logit model and mixed logit model to assess preferences and heterogeneity.Ethics and disseminationThe study findings have the potential to inform policies for STI treatment and management to align healthcare services with user preferences. This can improve STI healthcare access for young women in underserved communities. Ethical approval was obtained, and results will be disseminated through peer-reviewed journals and health conferences.Strengths and limitations of this studyDCEs provide a platform for users or consumers to express their preference for particular goods or services based on their attribute selection.Previously STI healthcare service provision has not been aligned with the preferences of young women. Therefore, this will reveal their preferences for a self-sampling intervention for STI healthcare and management.In instances where user preferences do not align with current practices for STI healthcare, this will provide an opportunity for policies to be reviewed and amended accordingly.This type of impact on STI healthcare aligns with goal 3.1 of South Africa’s National Strategic Plan which seeks to improve access to healthcare services for STIs and other diseases (1). It also aligns with goal three of the United Nations which seeks to improve access to healthcare for all and thus achieve universal healthcare coverage (2, 3).Since our study will be conducted on young women residing in underserved urban populations, our findings may not be a true reflection of young women from diverse communities.