Objectives: There are studies in the literature showing the clinical importance of fragmented QRS (fQRS) in many systemic diseases. In this study, we aimed to investigate the frequency and prognostic value of fQRS on electrocardiogram (ECG) in patients with acute ischemic stroke. Materials and methods: We prospectively enrolled 241 patients with acute ischemic stroke between January 2018 and January 2020. ST depression and elevation, QRS duration, PR interval, RR interval, QTc interval, QTc dispersion (QTcd), T negativity, Q wave, and fQRS were evaluated on ECG. Brain computed tomography (CT) and diffusion magnetic resonance imaging (MRI) images were obtained in the acute period and the National Institute of Health Stroke Scale (NIHSS) score was calculated for each patient. Patients were followed up for a period of two years. Results: The 241 patients comprised 121 (50.2%) men and 120 (49.8%) women with a mean age of 67.52 13.00 years. In Cox regression analysis, age, NIHSS, QTcd, and fQRS were found to be independent predictors of mortality (age, hazard ratio [HR]: 1.063, p < 0.001; NIHSS, HR: 1.116, p = 0.006; QTcd, HR: 1.029, p = 0.042; fQRS, HR: 2.048, p = 0.037). Two-year mortality was higher in patients with fQRS than in patients without fQRS (31% vs. 9%, p = 0.001). Conclusions: The fQRS is associated with poor prognosis in patients with acute ischemic stroke.