Inflammatory bowel disease (IBD) is a public health challenge and the use of pectin for symptom amelioration is a promising option. In this work, sunflower pectin has been extracted without (CHP) and with assistance of ultrasound (USP) using sodium citrate as a food-grade extracting agent. At optimal conditions (64 °C, 23 min) the highest yield was obtained with ultrasound application (15.5 vs. 8.1 %). Both pectins were structurally characterized by 1H NMR, HPSEC-ELSD, FT-IR and GC-FID. Unlike CHP, USP showed a lower molecular weight, higher galacturonic acid, lower degree of methyl-esterification and, overall, higher viscosity. These characteristics could affect the anti-inflammatory activity of pectins, evaluated using DSS-induced IBD model mice. So, USP promoted the defence (ICAM-1) and repair of the gastrointestinal mucosa (TFF3, ZO-1) more effectively than CHP. These results demonstrate the potential amelioration of acute colitis in IBD mice through USP supplementation. Taking into account the biomarkers analysed, these results demonstrate, for the first time, the positive impact of sunflower pectin extracted by ultrasound under very soft conditions on inflammatory bowel disease that might open up new possibilities in the treatment of this serious pathology.