Background A non-invasive tool for the assessment of ulcerative colitis (UC) activity is needed for treatment control. Purpose To determine the efficacy of intravoxel incoherent motion (IVIM) in assessing inflammatory activity in UC. Material and Methods In this prospective study, 20 adult patients underwent 3.0-T magnetic resonance imaging (MRI) IVIM diffusion-weighted imaging (DWI) with 10 b-values (0–900 s/mm2) 0–6 days after biopsies entailing colonoscopy. The inflammatory activity of large bowel segments was graded on endoscopy with Mayo score and on pathology with a six‑grade classification system. IVIM‑derived parameters (f, D, and D*) calculated from regions of interest placed within the bowel wall were correlated with both scores (56 and 34 bowel segments, respectively). Radiologists were blinded to endoscopy and pathology results. A T-test and Wilcoxon rank sum test was used in comparisons and receiver operating characteristic curve analysis was performed. Results Statistically significant differences were found between histopathologically inactive or mild activity and moderate to severe activity in f (respectively: mean = 0.19 and mean = 0.28, P = 0.024; area under the curve [AUC] = 0.723, sensitivity 0.82, specificity 0.59, accuracy 0.67 for a 0.185 cut-off value) and D (mean = 1.34 × 10−3mm2/s and mean = 1.07 × 10−3mm2/s, P = 0.0083; AUC = 0.735, sensitivity 0.91, specificity 0.54, accuracy 0.66 for cut-off value 1.24 × 10−3mm2/s). No significant difference in D* was noted. No significant correlation between Mayo endoscopic subscore, and f, D, nor D* was found. Conclusion IVIM perfusion fraction correlates with UC activity and might represent emerging tool in assessment of inflammatory activity.