This study proposes a mission-oriented framework for funding public research institutions (PRIs). Using a multi-case study approach and focus group interviews, a comprehensive framework was developed and refined. The framework encompasses three main dimensions: funding mechanisms, the amount of government funding, and organizational arrangements for resource allocation. It introduces diversified funding mechanisms for PRIs, including block grants, performance-based contracts, competitive funding, targeted allocations for specific missions, and excellence budgets. The proportion of each mechanism in the funding portfolio can vary depending on the mission types of PRIs. The framework recommends estimating government funding amounts using per capita formulas based on relevant input/output indicators tailored to the mission types of PRIs. Clear organizational arrangements are essential, including establishing a national research agency to oversee the estimation, steering, and monitoring of financial resource allocation and utilization.