Many animal species migrate over long distances, but the physiological challenges of migration are poorly understood. It has recently been suggested that increased molecular oxidative damage might be one important challenge for migratory animals. We tested the hypothesis that autumn migration imposes an oxidative challenge to bats by comparing values of 4 blood-based markers of oxidative status (oxidative damage and both enzymatic and nonenzymatic antioxidants) between Nathusius’ bats Pipistrellus nathusii that were caught during migration flights with those measured in conspecifics after resting for 18 or 24 h. Experiments were carried out at Pape Ornithological Station in Pape (Latvia) in 2016 and 2017. Our results show that flying bats have a blood oxidative status different from that of resting bats due to higher oxidative damage and different expression of both nonenzymatic and enzymatic antioxidants (glutathione peroxidase). The differences in oxidative status markers varied between sampling years and were independent from individual body condition or sex. Our work provides evidence that migratory flight might impose acute oxidative stress to bats and that resting helps animals to recover from oxidative damage accrued en route. Our data suggest that migrating bats and birds might share similar strategies of mitigating and recovering from oxidative stress.