Scutellaria baicalensis extracts (SBE) have demonstrated potential therapeutic effects against gastrointestinal disorders. This study evaluated the effects of SBE on zymosan-induced irritable bowel syndrome (IBS) symptoms and the underlying mechanisms involved. The major components of SBE, baicalin and baicalein, were quantified using high-performance liquid chromatography. SBE inhibited pacemaker potentials in interstitial cells of Cajal in vitro, with an IC₅₀ value of 27.48 μg/mL. In an animal model of IBS, SBE administration restored colonic length, weight, and stool consistency. Furthermore, SBE reduced tumor necrosis factor-α expression and alleviated pain-associated behaviors. Histological analysis revealed that SBE treatment restored normal colon tissue structure and significantly reduced inflammation. Electrophysiological recordings demonstrated that SBE inhibited the activity of transient receptor potential (TRP) channels, including TRPV1, TRPV4 and TRPA1, as well as voltage-gated sodium channels (NaV1.5), which are associated with visceral pain hypersensitivity. These findings suggest that SBE has therapeutic potential, making it a promising candidate for the management of IBS.