Background Computed tomography (CT) scan is one of the most frequent tests among children in which they should be completely calm and immobilized for a correct patient test. In this study, we aimed to investigate the effects of Intramuscular dexmedetomidine (DEX) with Intramuscular ketamine in children undergoing CT imaging. Materials and Methods This double-blind clinical trial study was conducted in Golestan and Imam Khomeini hospitals of Ahvaz, Iran, in 2017 and 2018. In the first and second groups, Intramuscular ketamine and Intramuscular DEX were injected with doses of 4 mg/kg and 3 μ g/kg, respectively. The objective of the drug injection was to reach the patient at a level of sedation of 4. During the entire period of sedation, heart rate and blood pressure were measured and recorded at the start of the study as well as after 5, 10, 15, 20, 25, 35, 45, and 55 minutes. Results In this study, 94 children needing sedation in CT-scan were included. The mean age of the children was 3. 87 ± 1. 70 years old and 54. 3% of them were girls. Mean time of onset of sedation in ketamine group (8. 82 ± 3. 86 minutes) was significantly lower compared to that of the DEX group (20. 46 ± 10. 9 minutes) (p < 0. 001). In addition, the mean duration of sedation effect in ketamine group was significantly lower than that of the DEX group (p = 0. 002). There was no significant difference in the mean discharge time in the two groups. In the ketamine group, 8 cases had side effects, however, no side effects were observed in the DEX group (p = 0. 006). Conclusion Based on the results, although DEX has a slower onset of effect and a longer duration of effect compared to ketamine, due to its lower side effects, it can be an appropriate alternative to commonly used sedative medications.