Objective: Dexmedetomidine has been shown to exert protective and curative effects on various tissues and organs in different pathological processes. This study aimed to investigate the effect of dexmedetomidine on the regeneration process after inducing a critical-sized bone defect in the calvarium of rabbits. Subject and Methods: Twenty-four male Oryctolagus cuniculus rabbits were divided into three groups, and an 8-mm circular parietal critical-sized bone defect was induced in all groups. Group_LD was given dexmedetomidine 2.75 µg/kg; Group_HD, dexmedetomidine 5.5 µg/kg; and Group_C, saline; all administered intraperitoneally for 7 days. The blood pressure and sedation score of the rabbits were evaluated. Bone tissue samples collected at the end of 8 weeks were examined via micro-computed tomography (micro-CT) and histomorphometry. Results: The micro-CT results indicated that regeneration significantly improved in all parameters in the dexmedetomidine-treated groups (p < 0.001). Furthermore, low-dose dexmedetomidine statistically significantly increased the bone volume ratio (BV/TV) compared with high-dose dexmedetomidine (p = 0.002). Trabecular thickness, connectivity value, and connectivity density were statistically significantly higher in Group_LD than in Group_HD (p < 0.001). The highest BA/TA% measurement in histomorphometry was observed in Group_HD, with a mean of 29.81% ± 8.52%. Significant intramembranous ossification was observed in the dexmedetomidine-treated groups, and active osteoblasts were observed in at the margin of the new bone trabeculae. Conclusion: This study demonstrated that dexmedetomidine increases osteoblastic activity and regeneration quality. In particular, low-dose dexmedetomidine exerted a more significant positive effect on the regeneration process and regenerative tissue quality than high-dose dexmedetomidine according to the micro-CT parameters.