The aim of this study was to confirm the anti-inflammatory effect and explore the adverse effects and underlying mechanisms of Prunella vulgaris L., which has been extensively used for hundreds of years in East Asia. Network pharmacology studies predicted that glucocorticoids (GCs), GC-targeting molecules, and brain-derived neurotrophic factor (BDNF) were intensively involved in the anti-inflammation and glucose intolerance. To attest the effects and underlying mechanisms, C57 male mice were randomly divided into 5 groups, control (C), dexamethasone (Dex), water extract of P. vulgaris (PE 35 or 70 mg), and PE (70 mg) + mifepristone (PEM). After a 3-week treatment, acetic acid-induced writhing and hot plate tests confirmed the peripheral and central analgesic effects, respectively. Plasma GCs and BDNF were significantly increased. Coincidently, plasma pro-inflammatory cytokines, including IL1β, IL6, and IL10, were decreased by PE treatment, which were blocked by the application of mifepristone ( P < 0.5). Western blots confirmed GC receptor (GR) translocation, and decreased cyclooxygenase 2 in the lumber spine by PE treatment. Food intake was impeded after a 4-week PE treatment, but the ratio of bodyweight gain to food intake was increased in a time-dependent manner. An intraperitoneal glucose tolerance test disclosed that PE treatment impaired glucose disposal in mice. Quantitative polymerase chain reaction (PCR) showed that hepatic GC-responsive genes such as GC-induced leucine zipper protein and glucose-6-phosphatase catalytic subunit 1 were up-regulated, and hypothalamic neuropeptide Y and agouti-related protein expressions were decreased by PE treatment. Hypothalamic BDNF was up-regulated, whereas hepatic BDNF was down-regulated. The regulation of these genes by PE was reversed by mifepristone administration. In conclusion, PE treatment plays analgesic and glucose regulation roles simultaneously through GC-induced signaling pathways, and P. vulgaris may provide a natural ligand of GR for the treatment of inflammation with glucose dysregulation.