Objectives Sexually transmitted infections (STIs) continue to cause substantial global morbidity and mortality, compounded by reliance on syndromic management and limited access to laboratory diagnostics. Although point-of-care tests (POCTs) can enable timely diagnosis and treatment, their adoption within health systems remains inconsistent. Here we present an implementation research protocol that aims to generate evidence on the acceptability, feasibility and suitability of a collaborative whole-system programme model to support implementation of STI POCTs and improve access to STI testing and treatment across diverse populations and settings. Methods This implementation research protocol describes a whole-system programme model for STI POCTs that can be locally adapted across multiple countries and is delivered through structured, interest-holder-led workshops. Participating sites will vary across sexual and reproductive health services, antenatal care and general practice. Sites will implement POCTs for Chlamydia trachomatis, Neisseria gonorrhoeae , Trichomonas vaginalis and/or HIV/syphilis for 1 year. A mixed-methods evaluation will assess patient clinical outcomes, health system capacity, economic costs and acceptability among patients, healthcare professionals and policymakers. Quantitative data will be collected before and after implementation alongside qualitative data from workshops, focus group discussions and interviews. A realist case-study comparison approach will examine mechanisms influencing implementation. Primary outcomes include changes in same-day diagnosis and appropriate treatment, patient and provider acceptability, service delivery capacity and incremental cost consequences compared with usual care. The evaluation will identify which components of the programme model are effective, for which services and under what circumstances, and will generate policy-relevant evidence on barriers and facilitators to POCT adoption. Conclusions This study addresses a key evidence gap in how to integrate STI POCTs sustainably within health systems. By combining local co-design, structured knowledge exchange and rigorous evaluation, the programme model has the potential to support equitable scale-up of STI POCTs and inform national policy and service delivery.