To identify proteins that are expressed at high levels in samples of cerebrospinal fluid (CSF) from Guillain-Barré Syndrome (GBS) patients and determine whether such proteins are involved in the pathogenesis of this disease, liquid chromatography-tandem mass spectrometry was performed to determine the proteome of GBS patients, and multiple sclerosis and cerebral infarction patients were arranged for case groups. We detected the samples of neuromyelitis optica Spectrum disorders (NMOSD) patients at the same time, but the results were not included in this article. The discovery set featured 5 patients, while the validation set featured 20 patients in each of the three groups. For validation set, every 10 samples were divided into a group and mix detection was performed, and each group was tested twice. To eliminate the potential influence of blood-borne proteins entering the CSF via the blood-brain barrier, we performed proteomics analysis in paired serum and CSF samples. This allowed us to identify a profile of proteins that were expressed in the CSF but not the serum. Functional enrichment analysis was performed by FunRich. We used the STRING website, along with Cytoscape and Molecular Complex Detection, to investigate the protein–protein interaction (PPI) network. In total, 135 and 231 proteins from the discovery and validation sets of GBS patients, respectively, were CSF-specific. Of these, 99 proteins were detected in both sets of samples. Several proteins play a key role in the regulation of Ca2+, including calmodulin, chromogranin-A, et al. The PPI network featured 84 nodes and 238 interactions; one significant module and 8 hub genes were identified. Several protein pathways that were closely related to Ca2+ regulation were found to be significantly enriched in CSF samples from GBS patients. Our data indicate that the pathogenesis of GBS may be associated with an imbalance of Ca2+.