Recent studies reported the feasibility of quantifying a reliable infarct core (IC) volume using multiphase computed tomography (mCTA) based on deep learning, however its prognostic value was not fully clarified. Therefore, we aimed to evaluate the prognostic value of mCTA-estimated IC volume in patients with acute ischemic stroke (AIS) after mechanical thrombectomy (MT). We retrospectively reviewed patients who underwent mCTA and MT for large vessel occlusion in middle cerebral artery and (or) internal carotid artery within 6 hours after symptom onset between January 2018 and November 2019. Patients were dichotomized into good (modified Rankin Scale [mRS] score, 0-2) and poor (mRS, 3-6) outcome groups. mCTA-estimated IC volume were generated based on a multi-scale three-dimensional convolutional neural network. Univariate, multivariate logistic regression and receiver operating characteristic (ROC) curve analyses were used to identify the independent variables, and evaluate their performances in predicting the clinical outcome. Of 44 included patients, 27 (61.4%) patients achieved good outcome. National Institutes of Health Stroke Scale scores at admission [NIHSSpre] (odds ratio [OR], 1.191; 95%confidence interval [CI], 1.028-1.379; P=0.020) and mCTA-estimated IC volume (OR, 1.076; 95%CI, 1.016-1.140; P=0.013) were found to be independently associated with functional outcome in patients with AIS after MT. After integrating NIHSSpre and mCTA-estimated IC volume, optimal performance (area under the ROC curve, 0.874; 95%CI, 0.739-0.954) could be obtained in predicting the clinical outcome. mCTA-estimated IC volume might be promising for predicting the prognosis, and assisting in making individualized treatment decision in patients with AIS.