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Introduction Ischemic stroke has high morbidity, disability and mortality rates. The effective treatments recommended by guideline have considerable limitations due to their strict range of adaptation and narrow time window. Acupuncture is an effective and safe treatment for ischemic stroke, and the mechanism may be related to autophagy. In this systematic review, we aim to summarize and evaluate the evidence of autophagy in acupuncture therapy for animal models of middle cerebral artery occlusion (MCAO). Methods Publications will be retrieved from the MEDLINE, Embase, Cochrane Library, Web of Science, CNKI, CBM, CVIP and Wanfang databases. We will include animal experimental studies of acupuncture for MCAO, and the control group will receive placebo/sham acupuncture or no treatment after model establishment. Outcome measures must include autophagy and will include neurologic scores and/or infarct size. The Systematic Review Center for Laboratory animal Experimentation (SYRCLE) risk of bias tool will be used to assess the risk of bias. A meta-analysis will be performed if the included studies are sufficiently homogenous. Subgroup analyses will be conducted according to different intervention types and different types of outcomes. Sensitivity analyses will also performed to explore the heterogeneity and to assess the stability of the results. Publication bias will be assessed by funnel plots. The Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) system will be applied to evaluate the quality of evidence in this systematic review. Discussion The results of this study may help to explain autophagy in acupuncture therapy for ischemic stroke. The limitation of this review is that all included studies will be retrieved from Chinese or English medical databases due to language barriers. Registration We registered in PROSPERO on May 31, 2022. (https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=329917) (CRD42022329917).