Aims: The purpose of this study was to examine and compare the association of baseline high-sensitive C-reactive protein (hsCRP) levels with Early Neurological Deterioration (END) in acute ischemic stroke with and without Atrial Fibrillation (AF). Methods: Consecutive ischemic stroke patients admitted to our center within 24 h of symptom onset were prospectively recruited. Plasma hsCRP levels were measured after admission and categorized into three groups (low risk, <1.0 mg/L; average risk, 1-3 mg/L; and high risk, >3 mg/L). END was defined as a National Institutes of Health Stroke Scale (NIHSS) score increased ≥ 2 during the first 72 h compared with the initial NIHSS score. Results: A total of 811 patients with ischemic stroke including 348 female with average age of 66.44 ± 12.54 y were enrolled in the analysis. Of them, AF was found in 226 (27.9%) patients. During the first 72 h after admission, 81 (35.8%) patients with AF and 181 (30.9%) patients without AF developed END, respectively. After adjusting the confounding factors whose P value<0.1 in univariate analysis, multiple logistic regression analysis demonstrated that high risk level of hsCRP (OR=2.39, 95% CI: 1.06-5.40) was the independent predictors of END in AF-related stroke. However, any level of hsCRP was found to be independently related to END in patients without AF. Conclusion: Our study demonstrated that high level of hsCRP independently correlated with END in AF-related ischemic stroke.