Acute pharyngitis is one of the most frequent causes of primary care physician visits; however, there is no agreement about which is the best strategy to diagnose and manage acute pharyngitis in children. The aim of the current study was to evaluate the cost-effectiveness of the recommended strategies to diagnose and manage acute pharyngitis in a paediatric population. A decision tree analysis was performed to compare the following six strategies: "treat all", "clinical scoring", "rapid test", "culture", "rapid test + culture" and "clinical scoring + rapid test". The cost data came from the Spanish National Health Service sources. Cost-effectiveness was calculated from the payer's perspective. Effectiveness was measured as the proportion of patients cured without complications from the disease and did not have any reaction to penicillin therapy; a sensitivity analysis was performed. The findings revealed that the "clinical scoring + rapid test" strategy is the most cost-effective, with a cost-effectiveness ratio of 50.72 . This strategy dominated all others except "culture", which was the most effective but also the most costly. The sensitivity analysis showed that "rapid test" became the most cost-effective strategy when the clinical scoring sensitivity was <91% and its specificity was ≤9%. In conclusion, the use of a clinical scoring system to triage the diagnoses and performing a rapid antigen test for those with a high score is the most cost-effective strategy for the diagnosis and management of acute pharyngitis in children. When the clinical scoring system has a low diagnostic accuracy, testing all patients with rapid test becomes the most cost-effective strategy.