Introduction: Each patient admitted to the hospital is subject to one medication error per day, since the occurrence of this one with the potential to cause harm is three times more common in pediatric hospitalized patients than in adults. These harms can result from inaccurate or incomplete drug use histories when patients undergo a clinical evaluation, which jeopardizes patient safety and compromises hospitalization costs. Thus, medication reconciliation (MC) emerges as a possible solution to avoid the occurrence of these in pediatric patients and directly contributes to reducing costs in the hospital environment and increasing quality of life). Therefore, this study proposes to determine whether pharmacist-led medication reconciliation is a cost-effective strategy to improve health outcomes in pediatric patients. Methods: A randomized clinical trial will be carried out, over eight months, to carry out the cost analysis. Micro-costing pharmacoeconomic model through a questionnaire and clinical interview to collect the variables necessary for the study and comparison of the control and intervention groups. Participants in this study will be children aged 0 days to 12 years, admitted to the hospital. The perspective adopted will be that of the hospital. To assess the economic outcomes of MC, the cost-effect pairs will be categorized and visually represented in the cost-effectiveness plan to compare the intervention and control groups. Monte Carlo simulation and univariate sensitivity analysis will be performed to test the robustness of the findings. Ethics and dissemination: The clinical trial was approved by the Research Ethics Committee of the Federal University of Sergipe (CAAE: 19625319.6.0000.5546 and opinion number: 3,630,579). This protocol fully adhered to the recommendations of the 2010 CONSORT Declaration and was registered in the Brazilian Registry of Clinical Trials (ReBEC): RBR-25dnqsk.