Ecological niche models (ENM) have been used to reconstruct potential distributions during the Last Glacial Maximum (LGM)—or other time periods—and this use is increasingly common in zoological studies. For this reason, we urgently need understanding factors affecting these predictions. Here, we examine how the use of different Global Circulation Models (GCMs) affects the variability in species' potential distributions during the LGM and how the degree of model extrapolation and its associated uncertainty depends on the GCM used. We develop these issues using two North American shrews, Notiosorex crawfordi and Cryptotis alticola, inhabiting two environmentally different regions. First, we compared paleoclimates in these two regions simulated by three GCMs: Community Climate System Model (CCSM), Model for Interdisciplinary Research on Climate (MIROC), and the Max‐Planck‐Institute für Meteorologie model (MPI). Then, we used maxent to estimate the LGM potential distribution of these two mammals under the three GCMs to assess the spatial variability and extrapolation uncertainty associated with idiosyncrasies of GCM. MIROC estimated noticeably more different climatic conditions than CCSM and MPI in the study areas during the LGM, and its pattern of environmental conditions was distributed differently. The MIROC scenario suggested a remarkable different prediction of potential distribution for both species, being more dramatic for the high mountain shrew, C. alticola. In particular, climatic differences among GCMs resulted in differences in the factors that limit and drive the potential distribution of the species during the LGM. Equally dramatic was the disagreement of extrapolation areas among GCMs. MIROC showed a greater number of pixels where extrapolation is required in both regions. Our findings should be taken into consideration when identifying areas of endemism, dynamic geographic barriers, and glacial refugia. When projecting into alternative scenarios of LGM climate, the idiosyncrasies of each GCM should be explicitly taken into account.