The process of morning awakening is associated with a marked increase in cortisol secretion, the cortisol awakening response (CAR), as well as with a burst in cardiovascular (CV) activation. Whilst the CAR is largely driven by awakening-induced activation of hypothalamic–pituitary–adrenal axis, it is fine-tuned by direct sympathetic input to the adrenal gland. In parallel, awakening-induced activation of the CV system is associated with a shift towards dominance of the sympathetic branch of the autonomic nervous system. Moreover, the CAR, in common with trait-like heart rate variability (HRV), is widely reported to be associated with psychosocial variables and health outcomes. These commonalities led us to examine associations between the CAR and both concurrent awakening-induced changes and trait-like estimates in cardiovascular activity (heart rate (HR) and HRV). Self-report measures of difficulties in emotion regulation and chronic stress were also obtained. Forty-three healthy participants (mean age: 23 years) were examined on two consecutive weekdays. On both days, heart interbeat interval (IBI) data was obtained from sedentary laboratory recordings as well as from recordings over the peri-awakening period. Salivary free cortisol concentrations were determined on awakening and 15, 30, and 45 min post-awakening on both study days. Data from a minimum of 36 participants were available for individual analyses. Results revealed significant awakening-induced changes in cortisol, HR and HRV measures; however, no associations were found between the simultaneous post-awakening changes of these variables. Similarly, awakening-induced changes in cortisol, HR and HRV measures were not significantly associated with perceived stress or measures of emotion regulation. However, the CAR was found to be significantly positively correlated with steady state measures of HR and negatively correlated with steady state measures of HRV, as determined during the laboratory sessions and the peri-awakening periods. This cross-sectional study indicates that, despite consistent associations between the CAR and indices of trait-like cardiovascular activity, the CAR is not related to concurrent changes of cardiac autonomic activation following awakening.