Ischemic stroke is a vascular disease that may cause cognitive and behavioral abnormalities. This study aims to assess abnormal brain function in ischemic stroke patients using the percent amplitude of fluctuation (PerAF) method and further explore the feasibility of PerAF as an imaging biomarker for investigating ischemic stroke pathophysiology mechanisms. Sixteen ischemic stroke patients and 22 healthy controls (HCs) underwent resting state functional magnetic resonance imaging (rs-fMRI) scanning, and the resulting data were analyzed using PerAF. Then a correlation analysis was conducted between PerAF values and Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA) scores. Finally, the abnormal PerAF values were extracted and defined as features for support vector machine (SVM) analysis. Compared with HCs, ischemic stroke patients showed decreased PerAF in the bilateral cuneus, left middle frontal gyrus, precuneus and right inferior temporal gyrus, and increased PerAF in the bilateral orbital part of middle frontal gyrus and right orbital part of superior frontal gyrus. Correlation analyses revealed that PerAF values in the left orbital part of middle frontal gyrus was negatively correlated with the MoCA scores. The SVM classification of the PerAF values achieved an area under the curve (AUC) of 0.98 and an accuracy of 94.74%. Abnormal brain function has been found among ischemic stroke patients, which may be correlated with visual impairment, attention deficits, and dysregulation of negative emotions following a stroke. Our findings may support the potential of PerAF as a sensitive biomarker for investigating the underlying mechanisms of ischemic stroke.