BACKGROUND: The global community has set an ambitious goal to end HIV/AIDS as a public health threat by 2030. Significant progress has been achieved in pursuing these objectives; however, concerns remain regarding the lack of disaggregated routine data for key populations (KPs) for a targeted HIV response. KPs include female sex workers, transgender populations, gay men and other men who have sex with men, people who are incarcerated, and people who use drugs. From an epidemiological perspective, KPs play a fundamental role in shaping the dynamics of HIV transmission due to specific behaviors. In South Africa, routine health information management systems (RHIMS) do not include a unique identifier code (UIC) for KPs. The purpose of this protocol is to develop the framework for improved HIV monitoring and programming through piloting the inclusion of KPs UIC in the South African RHIMS. OBJECTIVE: This paper aims to describe the protocol for a multiphased study to pilot the inclusion of KPs UIC in RHIMS. METHODS: We will conduct a multiphased study to pilot the framework for the inclusion of KPs UIC in the RHIMS. The study has attained the University of Johannesburg Research Ethics Committee approval (REC-2518-2023). This study has four objectives, including a systematic review, according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines (objective 1). Second, policy document review and in-depth stakeholder interviews using semistructured questionnaires (objective 2). Third, exploratory data analysis of deidentified HIV data sets (objective 3), and finally, piloting the framework to assess the feasibility of incorporating KPs UIC in RHIMS using findings from objectives 1, 2, and 3 (objective 4). Qualitative and quantitative data will be analyzed using ATLAS.ti (version 6; ATLAS.ti Scientific Software Development GmbH) and Python (version 3.8; Python Software Foundation) programming language, respectively. RESULTS: The results will encompass a systematic review of literature, qualitative interviews, and document reviews, along with exploratory analysis of deidentified routine program data and findings from the pilot study. The systematic review has been registered in PROSPERO (International Prospective Register of Systematic Reviews; CRD42023440656). Data collection is planned to commence in September 2024 and expected results for all objectives will be published by December 2025. CONCLUSIONS: The study will produce a framework to be recommended for the inclusion of the KP UIC national rollout. The study results will contribute to the knowledge base around the inclusion of KPs UIC in RHIMS data. TRIAL REGISTRATION: PROSPERO CRD42023440656; https://tinyurl.com/msnppany. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): PRR1-10.2196/55092.