Circadian disruption (CDR) is a chronic stressor that produces numerous adverse health consequences. Dietary prebiotics protect against acute stress and impact many of the same central nervous system (CNS) functions affected by CDR. Therefore, this study tested whether prebiotics could reduce the negative impacts of CDR on sleep architecture, cognition, and adrenal sensitivity. Male, Sprague Dawley rats consumed a prebiotic or control diet and were exposed to 8 weeks of CDR or a normal light/dark cycle. During week 9, sleep architecture, locomotor activity (LA), and core body temperature (CBT) were scored, cognitive testing performed, and plasma corticosterone and adrenal sensitivity measured. CDR impacted LA, CBT, NREM and REM sleep. Dietary prebiotics facilitated spatial learning and decreased plasma corticosterone, whereas both CDR and prebiotics decreased adrenal sensitivity. Finally, behavioral testing significantly disrupted sleep, which has implications for future animal research. These results demonstrate that both prebiotics and chronic CDR impact physiology and the CNS.