Bergenin is well-established and potent antioxidant compound with known gastro-protective effects. Main aim of the current investigation was to study the urease inhibitory potential of bergenin both experimentally and computationally. The target compound bergenin was isolated from acetone extract of Mallotus philippinensis bark. Bergenin inhibited the Bacillus pasteurii urease (IC50 value: 21.7 ± 0.2 lM). Thiourea was used as standard inhibitor (IC50 value: 25 ± 0.09 lM). Molecular docking studies revealed the potential binding mode of bergenin, according to which, Bergenin penetrated deeply into the active catalytic site of urease and was found in close interaction with nickel ions and the various important amino acid residues surrounding the catalytic site of B. pasteurii urease. This might be an additional gastro-protective mechanism by which, bergenin inhibits urease released by various urease producing bacterial strains especially Helicobacter pylori.