Increasingly diverse meal patterns affect the internal body clock. Ghrelin secretion is closely associated with the anticipation of a regularly scheduled mealtime, leading ghrelin to be a putative candidate for food-related entraining signals that drive activity rhythms. Here, growing pigs with different meal frequencies were used to construct an irregular eating pattern model. We found that irregular eating patterns changed central ghrelin levels of pigs, affected the circadian entrainment and circadian rhythm pathways in hypothalamus tissue, and altered the daily behavior and food anticipatory activity (FAA). To determine whether ghrelin exerts an effect, growing pigs were intravenously injected with ghrelin antagonist [D-Lys3]-GHRP-6 for 7 days. We showed here that [D-Lys3]-GHRP-6 administration decreased locomotor activity of growing pigs in the 4-h window preceding onset of food availability. In addition, we also confirmed that the direct role of ghrelin in molecular mechanism of regulating clock genes expression via calcium mobilization through intracellular PKC/PLC and AC/PKA pathways <i>in vitro</i>. Collectively, irregular eating patterns affect the central circadian system by ghrelin, supporting ghrelin as a temporal messenger of food-entrainment in hypothalamic circadian functions.