Introduction: For every healthcare system, provision and distribution of economic resources are among the most important issues. Development and economic growth of every country are dependent upon proper budgeting. Considering the role of budgeting in executive systems, especially in healthcare systems, budget system reforms can contribute to the improvement of a country's economy. One of the recent reforms in budgeting systems is the move towards "operational budgeting" which emphasizes on the assessment of government performance. However, evidence suggests that governments have faced challenges in the implementation of this budgeting system. This study aimed to identify and prioritize constraints and barriers which are affecting the implementation of operational budgeting in executive organizations of Sistan and Baluchestan province and provide solutions to remove these barriers. According to the existing literature and expert opinion, the barriers were classified into three categories: environmental factors, technical factors, and human factors.Methods: In this study, the sample included financial managers and government auditors of 28 operating systems in Sistan and Baluchestan province; these organizations (also known as the executive bodies of the province) received funds from the council of state development planning. Firstly, data were collected from library documents; this study attempted to gather expert opinion, as well. The data were collected via questionnaires, completed by 140 participants including financial managers, budget managers, financial controllers, financial analysts, and government auditors of executive bodies. For data analysis, Pearson’s correlation test, independent sample t-test, and one-way ANOVA were performed, using SPSS version 17. P-value£0.05 was considered statistically significant.Results: Mean and standard deviation (SD) of the total score of operational budgeting in the studied organizations were calculated as 158.28+14.38 in a total of 215 credits. The mean and SD for environmental, technical, and human factors were calculated as 51.15+5.50 out of 70 credits, 64.95+6.05 out of 90 credits, and 42.18+5.93 out of 55 credits, respectively. There was a significant relationship between operational budgeting challenges and each of the environmental, technical, and human factors (p£0.05).Conclusion: As the results indicated, environmental, technical, and human factors are obstacles to effective implementation of operational budgeting. In the ranking of these barriers, Friedman test showed that human factors play a more important role, compared to other factors. Therefore, employing efficient personnel with proper work background, education level, study major, experience, and expertise in budgeting and using expert consultants and workshops are essential for promoting operational budgeting.