The present study deals with challenges in the current structure of the Judiciary of the Islamic Republic of Iran regarding efficient allocation and proper management of financial resources. The findings of this descriptive and analytical study show that in effect the budgeting structure of Iran's Judiciary does not accept optimization and efficiency. Of major challenges of resource allocation are arbitrary allocation of resources regardless of long-term and middle-term planning, the lack of proper standards for measuring the performance of the plans and control of the results, the lack of fiscal discipline, the excessive influence of non-scientific bargaining and negotiations on the process of budgeting, relying merely upon incremental budgeting, failure to use of a suitable and efficient accounting system, the lack of accurate accounting information, the lack of transparency, and inefficiency of supervisory mechanisms of other powers on financial performance of the Judiciary. Also, the article proposes some suggestions and solutions to overcome such an undesirable situation.