Transportation investments determine the long-term success or failure of a transportation provider. It is therefore vital for decision makers to have an in-depth understanding of the alternatives available before they choose to invest. However, often, the process of evaluating alternatives is lengthy, costly, and contentious, particularly for transportation infrastructure investment decisions that are large, complex, and interconnected with other economic development and sustainability goals. Furthermore, transportation investments involve many decision makers, each with different priorities and expertise. Therefore, there is a need for transparent, accurate, flexible, and practicable decision-making aids that can handle the complex challenges facing the decision-making bodies of transportation providers and planning organizations. This paper introduces a new decision aid—the CLIOSjre Process—that combines insights from multicriteria decision analysis, multistakeholder negotiation theory, and uncertainty analysis. The CLIOSjre Process helps decision makers compare multiple alternatives across multiple objectives and seek an informed collective transportation investment decision. Unlike other multicriteria decision aids, the CLIOSjre Process accounts for differences of opinion among decision makers and is designed to facilitate constructive negotiation among them. Finally, the CLIOSjre Process formally accounts for sources of uncertainty inherent in these decisions. In this way, the CLIOSjre Process provides a unique and flexible framework for investment analysis that can adapt to changes in transportation alternatives, decision-maker priorities, and emerging real-world conditions. The usefulness of this new decision aid is illustrated for the East Japan Railway Company’s consideration of a transportation investment opportunity in high-speed rail development on the Northeast Corridor of the United States.