Almost daily we face stressful situations and the body reacts with various coping mechanisms. Consequently, glucocorticoids are released, leading to immunosuppression and a changed metabolism. However, if the stress becomes chronic, the coping systems can be maladaptively altered. In addition, glucocorticoid levels follow a daily circadian rhythm with a peak in the morning just before the organism starts to become active. While it is known that chronic stress can lead to a disruption of the circadian rhythm, it is still not fully understood how the long-term effects after chronic stress and the circadian rhythm interact on a molecular level. We address this question by assessing the transcriptome of the rodent hippocampus, a brain region critically involved in stress response behavior at the circadian high or low once a chronic stressor has subsided. We observe a persistent behavioral alterations as assed by automated tracking and sophisticated machine learning analysis, suggesting functional relevance of the disruption of circadian control of gene expression.