Southern flying squirrels (Glaucomys volans; SFS) nest in naturally formed cavities in snags and hardwoods found in mature, oak (Quercus spp.)–hickory (Carya spp.) forests. Intensive forest fragmentation of the Midwest United States limits the number of available nesting trees. We quantified annual nest‐site selection patterns by southern flying squirrels across fragmented landscapes of west‐central Illinois, USA. We used radiotelemetry to measure nest‐tree use by 55 SFS (30 males, 25 females) captured during 2014–2016. Of 105 nest trees used by SFS, live trees and snags comprised 75% and 25%, respectively. Probability of diurnal nest‐tree use increased 1.08/1.00‐cm increase in diameter‐breast‐height and by 1.50/1‐unit increase in the number of overstory mast trees between random and nest‐tree habitat areas (i.e., 300‐m2 circular plots). Similarly, probability of diurnal nest‐tree use increased 1.29/1‐unit increase in the number of snags between random and nest‐tree habitat areas. Our results revealed no intersexual differences in patterns of nest‐site selection, which may reflect the tendency for SFS to compensate for reduced availability of key structural attributes (i.e., snags, overstory trees) across fragmented forests by exhibiting similar intersexual patterns of nest‐tree use. Use of natural cavities for denning is encouraging, but also underscores the importance of unharvested oak–hickory forests in contributing essential habitat to SFS populations in fragmented Midwestern landscapes.