The expression of c-Fos protein has been extensively used as a marker of neuronal activation in response to stressful stimuli. Early maternal separation (MS) is a model of early life adversity that affects the responsiveness of the brain areas to stressors. Thus, this study examined the impact of early MS on activating stress-responsive areas in the brain of adult rats in response to physical (ether) or psychological (restraint) stressors. Male pups were divided for the MS or non-handled (NH) groups. The MS was carried out daily between the 2nd and 14th day of postnatal life and consisted in removing the dams from the cage for 180 min. The rats were then subjected to experimental protocols of restraint or ether exposure at 10–12 weeks old. The rats were anesthetized 90 min after exposure to the stressors, and their brains were prepared for immunohistochemical analysis of c-Fos immunoreactive (c-Fos-ir) neurons in the hypothalamic paraventricular nucleus (PVN), supraoptic nucleus (SON), medial preoptic area (MPA), medial amygdaloid nucleus (MeA), locus coeruleus (LC), and nucleus of the solitary tract (NST). The MS-group presented 86%, 125%, 73%, 56%, and 137% higher c-Fos-ir neurons in the LC, PVN, SON, MPA, and MeA, respectively, compared to NH-group in response to the restraint stressor. In addition, the MS-group presented 180%, 137%, 170%, and 138% higher c-Fos-ir neurons for the ether exposure in the LC, PVN, MPA, and MeA, respectively. Our results show a greater increase in neuronal activation in the MS group, indicating that early life adversity can induce reprogramming in the brain response to stress in adulthood.