Background With the use of sevoflurane, the incidence of emergence agitation (EA) has also increased. Objective We aimed to investigate whether S-ketamine can prevent EA after sevoflurane anesthesia in children. Methods Children undergoing otolaryngology surgery were assigned to one of four groups randomly. Drugs were given five minutes before the operation was accomplished. The incidence of EA was measured by the Pediatric Anesthesia Emergence Delirium Scale (PAED) scores. Face, Legs, Activity, Cry, and Consolability scale (FLACC) scores and the rate of adverse events were evaluated. Results The incidence of EA was significantly lower in children given 2 mg/kg propofol, 0.25 mg/kg S-ketamine and 0.5 mg/kg S-ketamine compared with that in children given normal saline. At 3 h and 6 h after operation, the FLACC scores in children given 0.25 mg/kg S-ketamine and 0.5 mg/kg S-ketamine were significantly lower than those in children given 2 mg/kg propofol and saline ( p < 0.001). No statistical differences were found in adverse reactions among children in the four groups. Conclusion Intravenous injection of propofol 2 mg/kg, S-ketamine 0.25 mg/kg and S-ketamine 0.5 mg/kg before end of the operation can all reduce the incidence of occurrence of emergence agitation in children undergoing tonsillectomy with or without adenoidectomy after sevoflurane anesthesia. Compared with children given propofol 2 mg/kg and S-ketamine 0.5 mg/kg, children given S-ketamine 0.25 mg/kg has the advantage of not prolonging the awakening time.