Introduction: Despite having the world's largest HIV epidemic, Sub-Saharan Africa (SSA) including South Africa (SA) has not yet achieved the 95-95-95 targets. To meet these targets, accurate and reliable key populations (KPs) disaggregated data is critical for guiding the HIV response. The inclusion of KPs Unique Identifier Code (UIC) on country routine health information management systems (RHIMS) can improve targeted resource allocation, reporting, and accountability. There is a gap in comprehensive review on how countries that implemented the unique identifier code went about in doing so. Methods and analysis A three-step search strategy will be utilized to get both published and unpublished documents. First, an initial search of MEDLINE identified keywords and MeSH terms. Second, a systematic search of electronic bibliographic databases including MEDLINE, PubMed, Scopus, PLOS ONE and Google Scholar, and thirdly, searching the reference list of all included reviews (hand-searching journals and reference tracking). Studies that meet the following PICO (Population, Intervention, Comparison, Outcome) criteria will be included: P: Published and unpublished materials reporting on key populations, namely men who have sex with men (MSM), sex workers (SW), people who inject/use drugs (PWI/UD), and transgender (TG); I: biometric fingerprint, alphanumeric code and any KPs UIC system; C: no unique identifier system; and O: KPs-specific 95-95-95 HIV cascade, KPs knowing HIV status, KPs on ART, ART adherence and Viral load suppression. This protocol was prepared using the Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P). References will be managed through ENDNOTE version 21 software. Two authors will screen the studies using Covidence software version 2.0 for inclusion according to the prescribed eligibility criteria. Differences will be addressed by consensus and with the assistance of an experienced third reviewer. Ethics and dissemination: This review will summarize findings from published studies containing non-identifiable data. The results will be disseminated via preprints, open-access peer-reviewed journals, and conference presentations. PROSPERO registration number: CRD42023440656