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BACKGROUND Melatonin and dexmedetomidine have both been used as a premedication to decrease emergence delirium in children. The effectiveness of oral melatonin, compared with atomised intranasal dexmedetomidine, in this role is not well studied. OBJECTIVE To study the efficacy of pre-operative atomised intranasal dexmedetomidine versus oral melatonin in children scheduled for ophthalmic surgery under sevoflurane. DESIGN A prospective, randomised, double-blind trial. SETTING Ophthalmic surgery in a university teaching hospital, April 2021 to October 2021. PATIENTS A total of 120 children undergoing ophthalmic surgery with sevoflurane anaesthesia. INTERVENTION Children were randomised to receive pre-operative intranasal dexmedetomidine 2 μg/kg via an atomiser device (dexmedetomidine group) or oral melatonin 0.5 mg kg−1 (melatonin group), 45 min before surgery. OUTCOMES MEASURED The primary outcome was the incidence of emergence delirium assessed by the Paediatric Anaesthesia Emergence Delirium scale. Secondary outcomes included pre-operative sedation, quality of inhalational induction, postoperative sedation and pain. RESULTS The incidence of emergence delirium was lower in the dexmedetomidine group than in the melatonin group (17 versus 37%, relative risk 0.45, 95% CI: 0.24 to 0.88; P = 0.01). Children in the dexmedetomidine group were more sedated following premedication and in the postanaesthesia care unit (P < 0.05). Postoperative pain scores were lower in the dexmedetomidine group than in the melatonin group: 0 [0 to 3] versus 2.5 [0–4], (P = 0.01). The requirement for and dose of rescue fentanyl analgesia postoperatively was comparable between the two groups. CONCLUSION Atomised intranasal dexmedetomidine significantly reduced emergence delirium in paediatric opthalmic procedures under sevoflurane anaesthesia compared to oral melatonin. TRIAL REGISTRATION Clinical Trials Registry of India CTRI/2021/03/032388 (www.ctri.nic.in)