One of 3 populations of the state‐threatened western gray squirrel (Sciurus griseus) in Washington occurs in the northern Cascade Range (i.e., North Cascades), where long‐term fire suppression has increased the risk of catastrophic wildfire. Land management agencies throughout this region have implemented fire fuel reduction programs that alter squirrel habitat and may affect their populations. From April 2008 to September 2011, we investigated resource selection of 38 radio‐collared western gray squirrels at 2 study sites in the North Cascades following fire fuel management activities including mechanical thinning and prescribed burning. We developed conditional logistic models to examine resource selection at 3 spatial scales: nest trees, nest sites, and core areas within home ranges. The odds of a squirrel selecting a tree for nesting increased with dwarf mistletoe (Arceuthobium spp.) presence, greater number of surrounding trees with interlocking branches, and tree size. Squirrels selected nest sites that had greater canopy cover, tree connectivity, and presence of dwarf mistletoe than available, unused sites. Core‐use areas within home ranges had greater canopy cover, a greater number of tree species, and trees with higher live crowns compared to low‐use areas. Our results indicate that fire fuel treatments may negatively affect western gray squirrel habitat across multiple spatial scales. Most variables that were positively related to habitat selection are specifically targeted for reduction in fire fuel management plans and were lower in sampled treated areas compared to untreated areas within the study sites. Key considerations in designing fuel reduction programs that benefit both squirrel habitat conservation and fire fuel management include maintaining forest patches with suitable canopy cover and connectivity, retaining large trees of a mix of species, and allowing for mistletoe infection at a reduced rate. © 2018 The Wildlife Society.