cAMP response element-binding protein (CREB) and nuclear factor kappa-B (NF-κB) are two ubiquitous transcription factors involved in a wide number of cellular processes, including the circadian system. Many previous studies on these factors use cellular assays that provide limited information on circadian activity or anatomical specificity. The ability to study transcription factors in defined tissue within intact animals will help to bridge the gap between cellular and in vivo data. We have used the GAL4-UAS and FLP-FRT systems to gain spatial control over reporter gene expression. Using a luciferase-based reporter, we show in vivo that Drosophila dCREB2- and NF-κB-mediated transcription oscillates in neuronal cells, glia, and in the mushroom body, a higher-order brain center in flies. This oscillation is under circadian control, cycling with a 24-hour rhythm, under both light-dark and dark-dark conditions. In light-light conditions, dCREB2 and NF-κB reporter flies exhibit a suppression of rhythmic activity. Furthermore, neuronal cycling of dCREB2 and NF-κB activity are modulated in period mutant flies, indicating these oscillations are controlled through the central clock. This study shows for the first time region-specific circadian oscillation of dCREB2/NF-κB activity in the Drosophila nervous system.