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Introduction: Intestinal ischemia-reperfusion (I/R) injury is a common clinical event. Mesenchymal stem cells (MSCs) have been widely used to repair intestinal injury in animal models. However, the effects of MSCs on intestinal I/R injury therapy remain unclear. Thus, we will perform a systematic review and meta-analysis of controlled trials to evaluate the efficacy of MSCs in animal models of intestinal I/R injury.Methods and analysis: We will search PubMed, Web of Science, Embase, Cochrane Library, Science Citation Index, China National Knowledge Information database, Wanfang Database, and the Chinese Scientific and Technological Journal Database in May 2021. We will include studies that evaluate the two different interventions for target MSCs to be maintained for the degree of histopathologic changes, mortality rate of rats, tumour necrosis factor α, and diamine oxidase. Two reviewers will independently screen titles and abstracts, perform a full article review, and extract study data. We will also use the SYRCLE tool to assess the risk of bias in the included studies. Furthermore, a random-effects meta-analysis will be conducted. Dichotomous and continuous outcomes will be analysed using risk ratios with 95% confidence intervals (CIs) and weighted mean difference with 95% CIs, respectively. For outcomes where different scales or different measurement methods have been used, the standardised mean difference will be applied. Subgroup and sensitivity analyses will be performed to explore the heterogeneity. Stata (version 12.0, Stata Corp, College Station, Texas, USA) will be used to analyse and pool the individual research results.Ethics and dissemination: This systematic review and meta-analysis does not require an ethical approval because no human beings are involved. We aim to publish this systematic review in a peer-reviewed journal.PROSPERO registration number: CRD42021231826