Background Hypertrophic Pyloric Stenosis (HPS) is one of the most common diseases requiring surgery in infants. Regardless of recruited surgical reconstruction techniques, preoperative evaluation, using proper anesthesia induction, perioperative, and postoperative care are the main determining factors in the outcome of these patients. This study aimed to evaluate and compare the premedication with intravenous fentanyl versus rectal acetaminophen on the anesthesia-related outcome of patients. Methods In this double-blinded randomized clinical trial, 24 infants who were managed to underwent a pyloromyotomy surgery due to the HPS were enrolled. Patients then randomly allocated into two groups of Fentanyl (F) or Acetaminophen (A). Anesthesia procedure was initiated with premedication with midazolam (0.03 mg/kg) co-administrated with fentanyl (1 µg/kg) in group F, and rectal acetaminophen (40 mg/kg) administrated 20 minutes prior to midazolam (0.03 mg/kg) in group A individuals. All patients’ vital signs, the period of each step of anesthesia, and the incidence of apnea were measured and recorded. Results Although the time duration from anesthesia termination till extubation and the recovery time were relatively shorter among the patients of the acetaminophen group, there were no statistically significant differences between the two groups. Patients in the acetaminophen group showed a lower level of pain in all evaluated timelines than those who were treated with fentanyl (p < 0.05). There was no statistically significant difference between the apnea incidence in two groups. Conclusion The use of rectal acetaminophen in infants who are planning to undergo pyloromyotomy due to HPS offers a better treatment outcome than fentanyl. Trial Registration: This study was approved by the Ethics Committee of Tabriz University of Medical Sciences under the registry code of IR.TBZMED.REC.1397.511. It was also registered in Iranian Registry of Clinical Trials (IRCT). The trial’s registration number (TRN) is IRCT20180726040601N1 ‘retrospectively registered’

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