Expression levels of circadian clock genes, which regulate 24-hour rhythms of behavior and physiology, have been shown to change with age. Using the colonial chordate Botryllus schlosseri, we combined transcriptome sequencing and stem cell-mediated aging phenomena to test how circadian gene expression changes with age. This revealed that B. schlosseri clock and clock-controlled genes oscillate globally with age-related daily amplitudes and frequencies. Age-specific, circadian patterns persist at the tissue level, where dramatic variations in gene expression of tissue profiles link to morphological and cellular aging phenotypes. Similar cyclical expression changes were found in hundreds of pathways associated with known hallmarks of aging. The atlas we developed points to alterations in circadian gene expression as a key hallmark of aging.