In humans, ischemic stroke is associated with reduced heart rate variability (HRV), a predictor of neurogenic cardiac events. This study was conducted to determine whether experimental stroke preferentially affects HRV during specific times of the day or parts of the sleep-wake cycle. A continuous telemetry system was used to analyze electroencephalograms (EEG), electromyograms (EMG), and electrocardiograms (ECG) after experimental ischemic stroke in rats (n = 13). Animals were implanted with telemetry probes and, after a two week stabilization period, 72h of baseline continuous EEG, EMG, ECG data were collected. Animals were then assigned to two procedure groups: 1) experimental stroke via 90 minute intraluminal filament occlusion of the right middle cerebral artery, or 2) sham surgery. Continuous waveform recording and HRV analysis was then continued for 48h following each procedure. HRV analysis was conducted by both time-domain and frequency-domain methods. Heart rate exhibited circadian rhythms among all animals prior to and following both procedures. Neither procedure contributed to significant heart rate changes. We did not find sleep state or circadian-dependent alterations in HRV in baseline recording. However, after stroke, animals exhibited elevated high frequency (HF) HRV (>10% increase, p<0.05) specifically during daytime waking periods. This contrasts with studies in humans that demonstrate reduced HRV after stroke, suggesting that age, medical comorbidities, or species differences modify the overall response to cortical infarction of autonomic control centers.