Project prioritization is often an arduous task for any organization. This is particularly evident in large, complex organizations with matrixed management structures, such as the VA Cooperative Studies Program (CSP). CSP is responsible for the planning and conduct of large multicenter clinical trials and epidemiological studies in the Department of Veterans Affairs (VA). CSP Health System Specialists (HSSs) have the primary responsibilities of facilitating alignment and coordination of program-level activities, and leading projects and initiatives to meet the goals of this clinical research program. There is an abundance of literature on Paired Comparison (PC) analyses to inform decision-making, but there is limited publicly available information on its use in clinical research administration settings. The purpose of this project was to determine the effectiveness of a PC analyses framework to inform decision-making in the context of the prioritization of projects assigned to or initiated by the CSP HSS group. Participants were nine HSSs that represented 9 of the 11 VA CSP Centers: 1 Clinical Research Pharmacy Coordinating Center (CRPCC), 3 Epidemiology Coordinating (EC) Centers, and 5 Clinical Trial (CC) Coordinating Centers. The CSP Program Manager also participated in this effort. Members were instructed by the HSS facilitator to complete two different versions of the PC worksheet in order to gain experience with using the PC method and to become familiar with its prioritization properties. The template for the PC worksheets was downloaded from www.mindtools.com. Participants were instructed to compare and rank predetermined values during the Values Paired Comparison exercise and projects of interest during the project Paired Comparison exercise. The Values PC exercise resulted in a clear ranking of the group's shared values, with "Safety" rising to the top. The subsequent results of the Project PC exercise, when stratified across the "EC HSSs" and "CC HSSs", showed that EC HSSs placed a higher value on projects that provided training for their role, while the CC HSSs placed higher value on projects that attempted to address program-level issues. When all participant scorings were tabulated together, three projects aimed at addressing program-level issues clearly rose to the forefront. This effort successfully utilized the PC analysis framework to prioritize a list of HSS projects. Using this framework allowed participants to prioritize a list of HSS projects. The framework also enabled the HSS group to identify shared values and to use them to assess the urgency and feasibility of group-assigned projects prior to investing time, effort, and funding in them. Lastly, this framework informed the need for further clarification and evaluation of identified projects as critical steps in project prioritization. There are numerous challenges to effectively performing decision-making in the context of prioritizing organizational projects, particularly in clinical research administration where shifting priorities are a constant. Therefore, the strategies outlined here may be beneficial and transferable to other clinical research administration settings, and beyond.