Controlled by the suprachiasmatic nucleus of the hypothalamus, circadian rhythm defines the day-night cycle in most animal species. We evaluated the effect of night and day cycle on the functional connectome by exploring a group of mice under light condition (LC) and another one under night condition (NC) using BOLD rs-fMRI. Our results show a significant increase in functional connectivity in NC group compared to LC group at the pineal gland level. This result is in line with this gland’s function. Furthers studies are needed to explore the effects of the circadian rhythm on both genders at different ages.