Appendectomy is still the best treatment for acute appendicitis in pediatric patients. Given the problems of early and immediate diagnosis of acute appendicitis, defining the best diagnostic protocol for this condition is of utmost importance. Different diagnostic methods, such as Lintula and appendicitis inflammatory response (AIR) scoring systems, are used for this purpose. This study aims to compare Lintula and AIR scoring systems among children with suspicion of acute appendicitis regarding their postoperative outcomes. During two years, a prospective multicentric study was carried out in the selected hospitals of Iran. Pediatric patients admitted with the diagnosis of acute appendicitis were enrolled in the study. Before decision making, each patient’s score was calculated according to two appendicitis scoring systems of Lintula and AIR. The clinical outcomes and diagnosis of patients were then compared to the results of each scoring system. For those patients who were a candidate to undergo surgery, the final diagnosis of acute appendicitis was made by histopathology. Patients were divided into high and low-risk groups according to scoring systems outcomes. Among the patients with lower scoring for appendicitis, the AIR scoring system had a sensitivity and specificity of 95%, which was more promising than that of the Lintula system (19%); however, the specificity was comparable between the two models (74% vs. 83%). For patients at higher risk of acute appendicitis, although the AIR scoring systems did not provide reliable results (sen: 45% and spe: 25%), the Lintula scoring showed remarkable sensitivity (87%), accompanied by a high diagnostic accuracy (87%). AIR and Lintula scoring systems are not accurate models to predict the risk of acute appendicitis among children; therefore, they can serve as an adjacent modality for other diagnostic methods.