Purpose <p>This prospective, quantitative, and correlative study aimed to evaluate the diagnostic performance of computed tomography enterography (CTE) as a noninvasive tool in detecting radiological markers of active inflammatory bowel disease (IBD) and to assess their correlation with clinical and endoscopic disease activity indices.</p> Results <p>Thirty patients with clinically and endoscopically confirmed IBD were prospectively enrolled. All participants underwent CTE as part of their diagnostic evaluation. The CTE results were correlated with clinical activity indices and endoscopic severity scores, which served as the reference standards. Mucosal enhancement, bowel wall thickening, and lymphadenopathy were the most accurate CTE indicators of active disease, each demonstrating a diagnostic accuracy of 96.7%. Significant correlations were observed between specific radiological findings and clinical disease activity scores—mucosal enhancement (<i>p</i> = 0.001), loss of vascular pattern (<i>p</i>  = 0.002), fat stranding (<i>p</i>  = 0.003), and lymphadenopathy (<i>p</i>  = 0.001). The inter-observer agreement for CTE findings was substantial, with a kappa value of 0.785.</p> Conclusion <p>CTE provides a reliable, noninvasive, and quantitative method for detecting active inflammation in IBD, effectively complementing with clinical and endoscopic markers particularly in acute or complicated scenarios. The study emphasizes the significance of specific CTE characteristics as quantitative indicators of disease activity, as well as a comprehensive assessment of associated extra-intestinal manifestations.</p>