Objective To compare the sedative effect of dexmedetomidine (Dex) by rectum administration or nasal administration in children before adenotonsillectomy. Methods A total of 85 children who were scheduled for adenotonsillectomy were enrolled. According to the random number table method, they were divided into two groups: a rectum administration group (group R, n=43) and a nasal administration group (group N, n=42). All children entered the operation waiting area 45 min before surgery. Children in group R were transrectally administered with Dex at 3 μg/kg, while those in group N were nasally administered with Dex at 3 μg/kg. Their heart rate and pulse oxygen saturation (SpO2) were recorded before administration (T0), 5 min (T1) and 10 min (T2) after administration and at the onset of sedation (T3). The sedative effects ［the onset time of sedation, the satisfaction rate of separation emotion, the satisfaction rate of venipuncture and the satisfaction rate of induction compliance checklist (ICC)］ were recorded. The satisfaction rate of medication in children, the score of parent satisfaction and awakening from anesthesia [the recovery time, the length of post‑anesthesia care unit (PACU) stay and the rate of postoperative emergence agitation] were recorded. Furthermore, adverse events such as bradycardia, hypotension, hypoxemia, nausea and vomiting, and laryngeal spasms from the time of administration to 2 h after operation were recorded. Results Compared with those at T0, both groups showed significant decreases in heart rate at T2 and T3 (P<0.05). There were no statistical differences in heart rate and SpO2 at each time point between the two groups (P>0.05). The satisfaction rate of medication in children and the score of parent satisfaction in group R were significantly higher than those in group N (P<0.05). There were no statistical differences in the onset time of sedation, the satisfaction rate of separation emotion, the satisfaction rate of venipuncture and the satisfaction rate of ICC, the recovery time, the length of PACU stay and the rate of postoperative emergence agitation (P>0.05). No adverse reactions such as bradycardia, hypotension, hypoxemia, nausea and vomiting, laryngospasm were reported in all the children from the time of administration to 2 h after operation. Conclusions Rectal administration of Dex has a similar sedative effect as intranasal administration, and can be used as an effective non‑invasive sedative method, which is more acceptable in children.