The relative roles of science and human values can be difficult to distinguish when informal processes are used to make complex and contentious decisions in wildlife management. Structured Decision Making (SDM) offers a formal process for making such decisions, where scientific results and concepts can be disentangled from the values of differing stakeholders. We used SDM to formally integrate science and human values for a citizen working group of ungulate hunting advocates, lion hunting advocates, and outfitters convened to address the contentious allocation of harvest quotas for mountain lions (Puma concolor) in west‐central Montana, USA, during 2014. A science team consisting of mountain lion biologists and population ecologists convened to support the working group. The science team used integrated population models that incorporated 4 estimates of mountain lion density to estimate population trajectories for 5 alternative harvest quotas developed by the working group. Results of the modeling predicted that effects of each harvest quota were consistent across the 4 density estimates; harvest quotas affected predicted population trajectories for 5 years after implementation but differences were not strong. Based on these results, the focus of the working group changed to differences in values among stakeholders that were the true impediment to allocating harvest quotas. By distinguishing roles of science and human values in this process, the working group was able to collaboratively recommend a compromise solution. This solution differed little from the status quo that had been the focus of debate, but the SDM process produced understanding and buy‐in among stakeholders involved, reducing disagreements, misunderstanding, and unproductive arguments founded on informal application of scientific data and concepts. Whereas investments involved in conducting SDM may be unnecessary for many decisions in wildlife management, the investment may be beneficial for complex, contentious, and multiobjective decisions that integrate science and human values.