This study examines the challenges of the Integrated Financial Management Information System (IFMIS) on fiscal management of public funds in ministry departments in Malawi. It also evaluates how public financial management systems can be improved through greater transparency and more equitable resource allocation. The study emphasizes the need for reforms that enhance the transparency of fiscal activities and ensure that resource distribution is aligned with the priorities of government departments. The research objectives were to identify challenges faced by IFMIS users, analyze optimal resource allocation, and determine the overall impact of IFMIS on public financial management. Data was collected using questionnaires from 50 respondents across various departments. The results showed that lack of training, coordination, and delays in civil servant salaries were the primary challenges. Recommendations include intensive training for personnel and improvements in network infrastructure to optimize the system's effectiveness.