Helicobacter pylori causes gastric and gastroduodenal ulcer disease and chronic infection of H. pylori is attributed to adenocarcinoma. 2-Substituted-5-(nitro-aryl)-1,3,4-thiadiazoles are being extensive evaluated against H. pylori isolates. In this study, a series of 2-Substituted-5-(5-nitro-furan-2-yl)-1,3,4-thiadiazoles selected and evaluated for anti-Helicobacter pylori activity. Molecular docking simulation on H. pylori urease active site improves showed potential interaction between selected ligands and H. pylori urease. In this study in vitro anti-Helicobacter pylori assay was evaluated for some selected 5-(5-nitrofuran-2-yl)-1,3,4-thiadiazole containing compounds. Docking simulation for designed compound was performed to explain mechanism of interactions. It was found that most compounds exhibited significant anti-Helicobacter pylori activity more potent than the standard drug metronidazole. In vitro anti-Helicobacter pylori activity was performed that 2-(5-(5-nitrofuran-2-yl)-1,3,4- thiadiazol-2-ylthio)-N-propylacetamide was the most potent compound among all tested compounds against clinical isolates of H. pylori. Development of new 5-(5-nitrofuran-2-yl)-1,3,4-thiadiazol derivatives containing thio-linker (N-(alkyl) acetamides) as potentially potent anti-Helicobacter pylori agents is greatly suggested.