Wogonin is a compound extracted from the medicinal plant Scutellaria baicalensis Geogi and has been found to exert antitumor activities in a variety of malignancies. However, the molecular mechanisms involved in the anti-gastric cancer (GC) effects of wogonin remain poorly understood. In the present study, we found that wogonin treatment inhibited the proliferation of GC cells, induced apoptosis and G0/G1 cell arrest, and suppressed the migration and invasion of SGC-7901 and BGC-823 cells in vitro. In addition, wogonin inhibited in vivo tumor growth in SGC-7901 xenograft mice. Transcriptomic analysis suggested that wogonin affected several signaling pathways closely related to tumor proliferation and metastasis, including the STAT3 signaling pathway. Further research indicated that wogonin may exert antitumor effects in GC cells by downregulating the JAK-STAT3 pathway. Altogether, our results demonstrate that wogonin exerts antitumor effects by perturbing JAK-STAT3 signaling in GC cells and that wogonin may be a potential therapeutic option for GC.