Infrastructures are the most fundamental facilities and systems serving the society. Due to the existence of infrastructures in economic, social, and environmental contexts, all lifecycle phases of such fundamental facilities should maximize utility for the designers, occupants, and the society. With respect to the nature of the decision problem, two main types of uncertainties may exist: 1) the aleatory uncertainty associated with the nature of the built environment (i.e., the economic, social, and environmental impacts of infrastructures must be described as probabilistic); and 2) the epistemic uncertainty associated with the lack of knowledge of decision maker utilities. Although a number of decision analysis models exist that consider the uncertainty associated with the nature of the built environment, they do not provide a systematic framework for including aleatory and epistemic uncertainties, and decision maker utilities in the decision analysis process. In order to address the identified knowledge gap, a three-phase modular decision analysis methodology is proposed. Module one uses a formal preference assessment methodology (i.e., utility function/indifference curve) for assessing decision maker utility functions with respect to a range of alternative design configurations. Module two utilizes the First Order Reliability Method (FORM) in a systems reliability approach for assessing the reliability of alternative infrastructure design configurations with respect to the probabilistic decision criteria and decision maker defined utility functions (indifference curves), and provides a meaningful feedback loop for improving the reliability of the alternative design configurations. Module three provides a systematic framework to incorporate both aleatory and epistemic uncertainties in the decision analysis methodology (i.e., uncertain utility functions and group decision making). The multi-criteria, probabilistic decision analysis framework is tested on a nine-story office building in a seismic zone with the probabilistic decision criteria of: building damage and business interruption costs, casualty costs, and CO2 emission costs. Twelve alternative design configurations and four decision maker utility functions under aleatory and epistemic uncertainties are utilized. The results of the decision analysis methodology revealed that the high-performing design configurations with an initial cost of up to $3.2M (in a cost range between $1.7M and $3.2M), a building damage and business interruption cost as low as $303K (in a cost range between $303K and $6.2M), a casualty cost as low as $43K (in a cost range between $43K and $1.2M), and a CO2 emission as low as $146K (in a cost range between $133K to $150K) can be identified by having a higher probability (i.e., up to 80%) of meeting the decision makers' preferences. The modular, holistic, decision analysis framework allows decision makers to make more informed performance-based design decisions—and allows designers to better incorporate the preferences of the decision makers—during the early design process.