: The current study focuses on autonomic nervous system activity during sleep as a physiological aspect of sleep quality, and investigated the associations between the cortisol awakening response (CAR) and autonomic activity during sleep and after awakening. Ambulatory electrocardiograms were obtained from 20 participants, who also provided saliva samples (at the time of awakening, and 30, 45, and 60 min after awakening) and rated the subjective quality of their sleep at home. Autonomic activity was assessed with the Lorenz plot indices, cardiac sympathetic index (CSI) and cardiac vagal index. Total salivary cortisol secretion after awakening was calculated as area under the curve with respect to ground (AUC(G)) and increase (AUC(I)). After controlling for confounding factors, including sleep duration and awakening time, cortisol AUC(G) and AUC(I) were both found to be negatively correlated with CSI during the 30 min before and after awakening: before (r = -0.526 and -0.601 respectively) and after (r = -0.540 and -0.493 respectively). Self-reported sleep quality was not associated with the CAR. These results suggest that the CAR is negatively affected by basal sympathetic activity immediately before and after awakening, but not affected by subjective sleep quality. Physiological arousals around the time of awakening might inhibit the CAR.