We quantified changes in density of red squirrels (Tamiasciurus hudsonicus) in response to prescribed fire in mixed coniferous forests of Idaho and Washington, USA, using a Before-After-Control-Impact design. We found no evidence that low-severity prescribed fires affected density of red squirrels; we estimated the change in red squirrel densities due to prescribed fire as −0.15 squirrels/ha (95% CI  =  −0.405–0.105). Squirrel density did, however, increase with increasing live tree density, shrub cover, and density of large downed logs, and varied across years and states. These results indicate that land managers implementing prescribed fire treatments to reduce fuel loads on public lands can reduce the impacts of fire on squirrel populations by formulating prescriptions to retain large live trees and large downed logs.