This study was designed to review published literature to determine the efficacy and safety of intranasal dexmedetomidine versus oral chloral hydrate (CH) for sedation in pediatric patients based on qualified studies. We searched the PubMed, Cochrane, and Embase databases for qualified studies published before March 2021. For each study, we analyzed the relative risk or weighted mean difference combined with a 95% CI. Fourteen studies including 3749 pediatric patients were included in this meta-analysis. Compared with oral CH, intranasal dexmedetomidine significantly increased the success rate of sedation and decreased the duration and latency of sedation, time of recovery from sedation, and total sedation time. Compared with oral CH, intranasal dexmedetomidine significantly decreased the incidence of adverse events, including vomiting, but increased the incidence of bradycardia. In conclusion, intranasal dexmedetomidine provides better sedation than oral CH for pediatric patients with good safety; however, the incidence of bradycardia is increased.