The present study was carried out to evaluate the effect of dietary supplementation of Scutellaria baicalensis extracts (SBE) on intestinal health in terms of morphology, barrier integrity and immune responses in weaned piglets challenged with Escherichia coli K88. A total of seventy-two weaned piglets were assigned into two groups to receive a basal diet without including antibiotic additives or the basal diet supplemented 1000 mg SBE/kg diet for 14 d. On day 15, twelve healthy piglets from each group were selected to expose to oral administration of either 10 ml 1 × 109 colony-forming units of E. coli K88 or the vehicle control. After 48 h of E.coli K88 challenge, blood was sampled, and then all piglets were killed humanely for harvesting jejunal and ileal samples. Dietary supplementation of SBE significantly decreased diarrhoea frequency and improved feed conversion ratio (P < 0·05). SBE supplementation to E.coli K88-challenged piglets improved villous height and villous height/crypt depth (P < 0·05), recovered the protein expression of occludin and zonula occludens-2 in both the jejunum and ileum (P < 0·05), and mitigated the increases in plasma IL-1β, TNF-α, IL-6, IgA and IgG (P < 0·05). Meanwhile, dietary SBE effectively inhibited the stimulation of NF-κB, P38 and TNF-α as well as IL-1β in the small intestine of piglets challenged by E. coli K88 and prevented the activation of NF-κB/P38 signalling pathways (P < 0·05). Collectively, SBE supplementation can potently attenuate diarrhoea in weaning piglets and decrease inflammatory cytokine expressions through inhibiting the NF-κB and P38 signalling pathways.