Operational auditing is an independent review including all aspects of an organization and an operational auditor has an overall objective to assess the quality of internal controls including its effectiveness and efficiency of operations, reliability of the financial reporting, and compliance with applicable laws and regulations. Operational auditing determines to what extent the manager has used the most efficient resources to achieve the most effective results. The aim of the research is to study whether applying risk-based audit would lead to increase the auditing efficiency process in operational auditing. In this research, Data Envelopment Analysis (DEA) technique has been used to measure the efficiency. We can calculate the efficiency by some inputs or outputs in DEA method. To compare the obtained efficiency of operational auditing by DEA, inferential, non-parametric (or distribution free) statistical tests are used. SPSS and LINGO software and Compare Means are used to measure the efficiencies in the research. T-test results for average efficiency comparison have been divided to both model and non-model states and show that the risk-based average efficiency is significantly more than the non-model state. It is therefore concluded that applying risk-based auditing model can increase operational auditing efficiency process in output-oriented method.