Upper endoscopy is a common procedure for the diagnosis and treatment of upper digestive tract diseases. The increasing number of pediatric gastrointestinal procedures has led to increasing attention on the safety and efficacy of medications used for sedation during the procedure. This randomized blinded interventional study was designed to compare the effect of oral midazolam with intravenous (IV) midazolam as a sedative medication in 119 children undergoing endoscopy. The mean time to sedation was 2.2±0.7 in IV midazolam group and 30.9±0 in oral midazolam group which was statistically significant difference between two groups. Separation from parents in oral midazolam group was as follow: 2 patients were high resistant (3.5%), 2 patients were resisted first and then relaxed (3.5%) and 55 patients were separated from their parents without any resistance (93%); whereas in IV midazolam group, 8 patients were high resistant (13.3%), 29 patients were relatively resistant (48.3%) and 23 patients were separated from their parents without any resistance (38.3%) that shows significant differences between the two groups. In terms of patient comfort during endoscopy, there was also a significant difference between the two groups. In oral midazolam, group parents were more consent, compared with the other group. The present study showed that oral midazolam is a safe and effective sedation during upper endoscopy in pediatrics. Oral midazolam reducing patientsʹ anxiety during separation from parents leads the easy use of endoscopy and comfort of patients during endoscopy as compared with IV midazolam. Oral or IV midazolam were not able to put most patients in deep sedation level.