Seismic risk management is concerned with complexity of diverse impacts and sorts of uncertainties involved in modeling, assessing and managing the earthquake risk. The way to handle uncertainty is a critical challenge in risk management and can mislead the overall decisions particularly in seismic risk mitigation programs where several projects are involved. Emergent complexity and uncertainties necessitate establishing a risk management system to address the risk in a reliable and realistic way. Current research proposes a heuristic model that combines both theoretically well-grounded system approach and risk analysis on a common framework. Hierarchical system approach is proposed to reduce the complexity of the risk inventory and turn it to set of manageable sub-systems. To capture uncertainties associated with observation and expert judgments, fuzzy modeling techniques was used. The applicability of the proposed models was tested over a group of retrofitting schools. Unlike conventional risk assessment methods, the methodology demonstrated more transparency and flexibility in practice.