Microcirculatory dysfunction plays a crucial role in renal ischemia/reperfusion (IR)-induced injury. Dexmedetomidine was reported to ameliorate IR-induced acute kidney injury. This study investigated the effects of dexmedetomidine on renal microcirculation after IR-induced acute kidney injury in rats. In total, 50 rats were randomly allocated to the following five groups (10 in each group): Sham, ControlIR, Dex (dexmedetomidine) Sham, DexIR, and IRDex group. The microcirculation parameters included total small vessel density, perfused small vessel density (PSVD), proportion of perfused small vessels, microvascular flow index, and tissue oxygen saturation (StO(2)) were recorded. The repeated measures analysis showed that PSVD on renal surface was higher in the DexIR group than in the ControlIR group (3.5 mm/mm(2), 95% confidence interval [CI] 0.6 to 6.4 mm/mm(2), P = 0.01). At 240 min, StO(2) on renal surface was lower in the ControlIR group than in the Sham group (- 7%, 95% CI-13 to-1%, P = 0.021), but StO(2) did not differ significantly among the Sham, DexIR, and IRDex groups. Our results showed that pretreatment with dexmedetomidine improved renal microcirculation in rats with IR-induced acute kidney injury. However, the adverse effects of low mean arterial pressure and heart rate might offset the protective effect of dexmedetomidine on organ injury.