Background Mechanical thrombectomy is the standard of care, in selected patients, for acute ischemic stroke with large vessel occlusion but its use in patients with stroke secondary to infective endocarditis is controversial. We report three cases of acute ischemic stroke treated by mechanical thrombectomy and we propose an extensive review of the literature to evaluate the clinical safety and efficacy of thrombectomy in patients with stroke secondary to infective endocarditis. Methods A comprehensive literature search was performed following a pre-specified protocol of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement. Case reports, cases series, cross-sectional studies, case control studies, randomized controlled trials or nonrandomized controlled trials were considered that included endocarditis-related acute ischemic stroke patients who underwent mechanical thrombectomy. Results The database search yielded 431 relevant records published until January 2020. Nineteen articles fulfilled the eligibility criteria that described thirty patients. After the thrombectomy, 13.3% of the patients experienced intracranial haemorrhage. After the procedure, the median National Institutes of Health Stroke Scale score dropped from 15 (IQR 7) to 2.5 (IQR 5.75). At 90 days, mortality was 23.3% while 46.7% of the patients were functionally independent (mRS ≤ 2). Discussion Based on our review, the use of mechanical thrombectomy in patients with large vessel occlusion due to endocarditisassociated stroke might improve patient outcome but it should be considered on a case by case base as the safety has not been well established yet. Further research on risk stratification is needed to drive clinician during the decision-making process.