Our objective was to compare the diagnostic accuracy of Alvarado and appendicitis inflammatory response (AIR) scoring systems among children suspected of acute appendicitis concerning their postoperative outcomes. During a two-year period, a prospective multicentric study was carried in the selected hospitals of Iran. All children who were admitted with the diagnosis of acute appendicitis were enrolled in the study. However, patients suffering from generalized peritonitis or those who had a history of abdominal surgery were excluded. Before decision-making, each patient’s score according to two appendicitis scoring systems was calculated. The clinical outcomes and diagnosis of patients were then compared to the results of each scoring system. For those patients who were a candidate for surgery, the final diagnosis of acute appendicitis was made by histopathology. Patients were divided into a high- and low-risk group according to scoring systems outcomes. Among the patients with a low score for appendicitis, the AIR scoring system had a sensitivity and specificity of 95% and 74%, respectively, which was more promising in comparison to that of the Alvarado system (90% and 70%, respectively). Regarding the patients at higher risk of acute appendicitis, none of the scoring systems provided reliable results since both systems showed sensitivity and specificity of less than 50%, which was not sufficient to distinguish patients who are a candidate for surgery. AIR and Alvarado scoring systems are not accurate models to predict the risk of acute appendicitis among children; however, the AIR system could be used as a reliable material to rule out the acute appendicitis diagnosis.