Brain metabolomics is an emerging field that complements the more traditional approaches of neuroscience. However, typical brain metabolomics workflows require that animals be sacrificed and tend to involve tedious sample preparation steps. Microdialysis, the standard technique to study brain metabolites in vivo, is encumbered by significant limitations in the analysis of hydrophobic metabolites, which are prone to adsorption losses on microdialysis equipment. An alternative sampling method suitable for in vivo brain studies is solid-phase microextraction (SPME). In SPME, a small probe coated with a biocompatible polymer is employed to extract/enrich analytes from biological matrices. In this work, we report the use of SPME and liquid chromatography-mass spectrometry for untargeted in vivo analysis of rodent's brains after deep brain stimulation (DBS). First, metabolite changes occurring in brain hippocampi after application of 3 h of DBS to the animals' prefrontal cortex were monitored with the proposed approach. As SPME allows for nonlethal sampling, the same group of animals was sampled again after 8 days of daily DBS therapy. After acute DBS, we detected changes in a broad range of metabolites, including the amino acid citrulline, which may reflect changes in nitric oxide production, as well as various phospho- and glycosphingolipids. Measurements conducted after chronic DBS showed a decrease in hippocampal corticosterone, indicating that DBS may have a regulatory effect in the hypothalamic-pituitary-adrenal axis. Our findings demonstrate the potential of in vivo SPME as a tool of scientific and clinical interest capable of revealing changes in a wide range of metabolites in brain tissue.