Background: Comparison of midazolam and propofol has been done hoping to reduce the incidence rates of emergence agitation (EA) after anesthesia. Both drugs however, are still under inspection as for their effect on EA after using Isoflurane for maintenance of anesthesia. Objectives: This study was designed for measuring the effect of either propofol or midazolam near the end of tonsillectomy operation on incidence of EA during the recovery phase. Methods: In this randomized, double-blind study, 90 children, aged 5 to 15, undergoing anesthesia with Isoflurane were randomly assigned to three groups receiving either propofol (group P), midazolam (group M) or saline (group S) near the end of anesthesia. Severity and incidence of EA were then calculated using the pediatric anesthesia emergence delirium (PAED) scale. Results: The mean PAED score in group P was (2.87 ± 2.69) and (1.90 ± 2.55) in group M. Both were significantly lower than group S (7.60 ± 3.78) (P < 0.05). However, there was no statistical difference in the duration of post-anesthesia care unit (PACU) stay between groups P (42.50 ± 12.58) and M (48.33 ± 24.26), groups P and S (52.00 ± 10.64) and between groups M and S (P > 0.05). No significant difference was found between all groups for apnea and laryngospasm (P > 0.05). Conclusions: Administration of either midazolam or propofol near the end of operation may result in reduction of EA in children undergoing tonsillectomy after Isoflurane anesthesia.