Background & Objective: Atrial fibrillation (AF) is the most common cardiac arrhythmia associated with risk of ischemic stroke. Atrial electrophysiological properties are influenced by alteration of cardiac autonomic tone. Cardiac autonomic derangement was reported in acute ischemic stroke patients. Atrial activity analysis with sample entropy (SampEn) and atrial fibrillatory rate (AFR) are the useful tools for evaluation of atrial electrophysiological properties. Heart rate variability (HRV) is a good indicator for cardiac autonomic function. We aimed to evaluate atrial activity by SampEn and AFR correlated with HRV in AF patients with acute ischemic stroke compared to which in AF patients with previous ischemic stroke. Methods and Results: Patients (age 69+10 years, n=40) were recruited, thereafter HRV, AFR, and SampEn were analyzed from surface electrocardiogram (ECG). Acute stroke group showed significant decreases in standard deviation of normal-to-normal intervals (SDNN), normalized low frequency (LF) and high frequency (HF) power (138+36 ms vs. 170+61 ms, 13+4 vs. 18+8 and 34+8 vs. 46+15, respectively) compared to post-stroke group. However, there was no significant difference in the LF to HF power (LF/HF) ratio between these two groups (0.41+0.14 vs. 0.43+0.24). Moreover, SampEn did not alter after stroke recovery, while AFR tended to decrease. Conclusions: Atrial electrophysiology properties by SampEn and AFR are not influenced by cardiac autonomic derangement during acute ischemic stroke period.