The circadian clock system in mammals drives many physiological processes including the daily rhythms of sleep–wake behavior, hormonal secretion, and metabolism. This system responds to daily environmental changes, such as the light–dark cycle, food intake, and drug administration. In this review, we focus on the central and peripheral circadian clock systems in response to drugs, food, and nutrition. We also discuss the adaptation and anticipation mechanisms of our body with regard to clock system regulation of various kinetic and dynamic pathways, including absorption, distribution, metabolism, and excretion of drugs and nutrients. “Chrono-pharmacology” and “chrono-nutrition” are likely to become important research fields in chrono-biological studies.