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Introduction Humanitarian emergencies, of either natural or anthropogenic origins, are equivalent to major disasters, which can lead to population displacement, food insecurity and health system disruptions. Almost two-thirds of people affected by humanitarian emergencies inhabit malaria endemic regions, particularly the WHO African Region, which currently accounts for 93% and 94% of malaria cases and deaths, respectively. As of late 2020, the United Nations Refugee Agency estimates that there are globally 79.5 million forcibly displaced people, including 45.7 million internally displaced people, 26 million refugees, 4.2 million asylum-seekers and 3.6 million Venezuelans displaced abroad.Methods and analyses A systematic review and meta-analysis will be conducted to evaluate the impact of different vector control interventions on malaria disease burden during humanitarian emergencies. Published and grey literatures will be systematically retrieved from 10 electronic databases and 3 clinical trials registries. A systematic approach to screening, reviewing and data extraction will be applied based on the Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines. Two review authors will independently assess full-text copies of potentially relevant articles based on inclusion criteria. Included studies will be assessed for risk of bias according to Cochrane and certainty of evidence using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. Eligible studies with reported or measurable risk ratios or ORs with 95% CIs will be included in a meta-analysis. Subgroup analyses, including per study design, emergency phase and primary mode of intervention, may be performed if substantial heterogeneity is encountered.Ethics and dissemination Ethical approval is not required by the London School of Hygiene and Tropical Medicine to perform secondary analyses of existing anonymous data. Study findings will be disseminated via open-access publications in peer-reviewed journals, presentations to stakeholders and international policy makers, and will contribute to the latest WHO guidelines for malaria control during humanitarian emergencies.PROSPERO registration number CRD42020214961.