Ulcerative colitis (UC) is a kind of persistent inflammatory bowel disease that is a root cause for lifelong soreness in the colon and rectum inflammation. Nuclear transcription factor kappa B (NF-κB) has a pivotal role in UC by regulating the expression of a variety of pro-inflammatory and proliferative genes. Its over-expression backs the process of cell proliferation, carcinogenesis leading to progression of cancer; thus, NF-κB might be an appropriate target for drug development. Therefore, identifying anti-inflammatory compounds can prove to be an operative approach to target inflammatory disorders. We employed molecular docking and molecular dynamics simulations and in vivo approach. The anti-inflammatory compounds of plant origin were screened using a molecular docking and dynamics simulation approach, and then, in vivo studies were conducted in acetic acid-induced UC in rats to examine their pharmacological potency. In silico study revealed the identification of potential compounds such as embelin and ginkgetin (a major constituent of Ginkgo biloba) in comparison to the standard drug sulphasalazine. Furthermore, the shielding effect of Ginkgo biloba extract formulation and embelin (25 & 50 mg/kg, p.o) was evaluated in acetic acid-induced colitis in rats. The in vivo study showed a noteworthy reduction in the activity of colonic myeloperoxidase and lower levels of lipid peroxidation and lactate dehydrogenase in serum, as well as a significant increase in glutathione. Furthermore, histopathological analysis confirmed the observed beneficial activity. This study provides the feasibility of ginkgetin and embelin as credible drug candidates for treating UC with dynamic pharmacological properties.