Microcirculatory disorders are one of the most common systemic alterations in septic patients, which can occur even in the presence of normal macro-hemodynamic parameters. Several anesthetic protocols have been indicated for sepsis. A drug frequently used in critically ill human patients is dexmedetomidine, a potent and selective alpha 2-agonist with sedative, analgesic and muscle relaxant properties that promotes blood pressure increase and peripheral vasoconstriction. The objective of the present study was to compare dexmedetomidine and fentanyl constant rate infusions in septic dogs using microcirculatory, hemodynamic and metabolic parameters. Thirty-three bitches with pyometra submitted to therapeutic ovariohysterectomy (OHE) and triaged with the quick SOFA score were included in the study. The animals were randomized into two groups treated with either dexmedetomidine (3 μg/kg/h) or fentanyl (5 μg/kg/h) constant rate infusions during isoflurane anesthesia and under mechanical ventilation. Hemodynamic, microcirculatory, ventilatory and metabolic parameters were recorded before, during and after anesthesia. The data were submitted to a normality test, then groups were compared using the unpaired Wilcoxon test or the t student test when necessary. All microcirculatory parameters were not significantly different between groups. Dexmedetomidine constant rate infusion provided superior blood pressure values and lactate clearance results, suggesting that it did not impair peripheral oxygen transport and organ perfusion, and both groups had similar clinical outcomes such as mortality and occurrence of hypotension and bradyarrhythmias. Similar values of microcirculatory parameters and higher blood pressure demonstrated that dexmedetomidine does not compromise microcirculation compared to fentanyl, it improves macro-hemodynamics instead.