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This paper presents a developed web-based decision support system that implements a multi-criteria decision analysis, the Analytic Network Process (ANP) as a modeling tool in screening and selecting an agency’s priority projects for inclusion in the annual budget proposal. Screening and selecting priority projects for inclusion in the annual budget proposal of the government is complex decision-making that involves many stakeholders with conflicting priorities and dynamic preferences and limited technical information. Government decision-making becomes more complicated because of the complexities carried by the people involved in the process and other factors contributing to balancing political, technical, and economic considerations. The application of Multi-Criteria Decision Analysis (MCDA) methods for decision-makers helps them facilitate the systematic treatment of information, inform those involved in the process, and develop effective decisions in complex circumstances. The development of a decision support system that implements MCDA tools such as Analytic Network Process (ANP) modeling techniques in screening and selecting priority projects helps manage this complexity and makes decision-making efficient, effective, and transparent. The study used a pre-defined set of criteria identified during the progress of the study.