Adverse life experience increases the lifetime risk to several stress-related psychopathologies, such as anxiety or depressive–like symptom following stress in adulthood. However, the neurochemical modulations triggered by stress have not been fully characterized. Neuropeptides play an important role as signaling molecules that contribute to physiological regulation and have been linked to neurological and psychiatric diseases. However, little is known about the influence of stress on neuropeptide regulation in the brain. Here, we have performed an exploratory study of how neuropeptide expression at adulthood is modulated by experiencing a period of multiple stressful experiences. We have targeted hippocampus and prefrontal cortex (PFC) brain areas, which have previously been shown to be modulated by stressors, employing a targeted Liquid Chromatography-Mass Spectrometry (LC-MS) based approach that permits broad peptide coverage with high sensitivity. We found that in the hippocampus, Met-enkephalin, Met-enkephalin-Arg-Phe and Met-enkephalin-Arg-Gly-Leu were up regulated, while Leu-enkephalin and Little SAAS were down regulated after stress. In the PFC area, Met-enkephalin-Arg-Phe, Met-enkephalin-Arg-Gly-Leu, peptide PHI-27, somatostatin-28 (AA1-12) and Little SAAS were all down regulated. This systematic evaluation of neuropeptide alterations in hippocampus and PFC suggests that stressor impact neuropeptides and that neuropeptide regulation is brain area specific. These findings suggest several potential peptide candidates, which warrant further investigations in terms of correlation with depression-associated behaviors.