IntroductionThe COVID-19 pandemic has significantly shaped the global landscape and impacted various aspects of individuals’ lives, especially the behaviour of school-going adolescents regarding substance use. Among these substances, alcohol is the most predominant substance, particularly among school-going adolescents, who also are highly susceptible to harmful alcohol use, such as poor academic performance, psychiatric disorders and disrupted social lives. This review will synthesise the known prevalence estimates and associated factors of alcohol use among school-going adolescents in the Southern African Development Community (SADC) since the COVID-19 pandemic.Methods and analysisWe will perform a systematic review in line with the Cochrane Handbook for Systematic Reviews. We will systematically search for selected global databases (ScienceDirect, EbscoHost, PsycINFO and PubMed) and regional electronic databases (African Index Medicus, Sabinet and African Journals OnLine). Peer-reviewed literature published between 11 March 2020 and 10 March 2024 will be considered for eligibility without language restriction. All 16 countries of the SADC region will be included in the review. The Mixed-Methods Appraisal Tool checklist for quality appraisal will be used to appraise the methodological quality of the included studies. Depending on the level of heterogeneity, prevalence estimates will be pooled in a meta-analysis; narrative synthesis will be applied to describe the reported associated factors of alcohol use.Ethics and disseminationWe will not seek ethical approval from an institutional review board since the study will not involve gathering data directly from individual school-going adolescents, nor will it violate their privacy. When completed, the full report of this review will be submitted to a journal for peer-reviewed publication; the key findings will be presented at local and international conferences with a partial or full focus on (adolescent) alcohol (mis)use.PROSPERO registration numberCRD42023452765.