Perioperative stress affects the outcome of carotid endarterectomy performed under regional anesthesia. Here we aimed to explore the temporal profile of the stress marker cortisol and its relationship to high-sensitivity troponin-T, matrix metalloproteinase-9, tissue inhibitor of metalloproteinase-1, and S100B as an indicator of blood-brain barrier alteration in the systemic circulation. Prospective part of the study: a total of 31 patients with significant carotid stenosis scheduled for carotid endarterectomy in regional anesthesia were enrolled. Follow-up part of the study and retrospective analysis of the outcome: each patient was followed up to five years and morbidity as well as mortality data were collected from an electronic database. Blood samples from each patient were serially taken; prior to surgery (T1), at the time of reperfusion (T2), 24 h (T3) and 72 h later postoperatively (T4), then the plasma concentration of each biomarker was measured. Besides, the clinical and surgical factors and perioperative adverse events were recorded. More positive correlations were found between: the early change of S100B (T2-T1) and late change in plasma cortisol level (T4-T3) (r = 0.403; p < 0.05); the early change of cortisol (T2-T1) and the early postoperative change of plasma matrix metalloproteinase-9 level (T3-T2) (r = 0.432; p = 0.01); the plasma concentration of tissue inhibitor of metalloproteinase-1 at 24 postoperative hours and the late change in plasma high-sensitivity troponin-T level (T4-T3) (r = 0.705; p < 0.001). Five patients needed an intraoperative shunt in whom the high-sensitivity troponin-T was elevated even prior to surgery, but definitive stroke never occurred. Plasma matrix metalloproteinase-9 concentration at reperfusion independently predicted the five-year mortality with a cut-off value of 456 ng/ml (sensitivity: 86%, specificity: 84%, area 0.887, p = 0.002). A higher intraoperative change in S100B level reflecting carotid endarterectomy induced acute silent brain ischemia was associated with more pronounced post-operative change of cortisol. An early elevation of cortisol was found to be associated with a delayed increase of matrix metalloproteinase-9. Importantly, an increased high-sensitivity troponin-T even prior to carotid endarterectomy may predict clamp intolerance, and elevated matrix metalloproteinase-9 at reperfusion suggests a poor outcome.