This study investigates audit challenges in Rwandan public hospitals, focusing on budget execution. Using a qualitative case study methodology, data were collected from secondary sources, including government and audit reports from 2008 to 2012. Statistical analysis revealed significant issues such as discrepancies averaging 460 million RWF between allocated and actual expenditures (t = 8.15, p < 0.01), inadequate staffing with only 47.6% of required auditors available by 2012, and declining adherence to procurement procedures (compliance dropped from 80% in 2008 to 60% in 2012). Furthermore, logistic regression demonstrated that improved procurement compliance reduced misallocation likelihood by 40% (p < 0.001). These findings underscore the urgent need for reforms in financial reporting, auditor capacity building, and enforcement of procurement standards. Recommendations include streamlining reporting systems, increasing auditor training, and enhancing oversight mechanisms to promote transparency and accountability in public healthcare financial management.