Helicobacter pylori (H. pylori) is a Gram-negative bacterium that colonizes the gastric mucosa and plays a central role in the development of peptic ulcers, chronic gastritis, and gastric cancer. A significant portion of the global population is infected, emphasizing the need for early detection and effective treatment strategies. Natural compounds, especially green tea flavonoids (GTFs), have recently gained attention as promising anti-H. pylori agents. Among them, Epigallocatechin Gallate (EGCG), the major catechin in green tea, shows notable inhibitory effects on H. pylori growth and colonization through mechanisms such as membrane disruption, enzyme inhibition, and oxidative stress modulation. Additionally, the antioxidant and anti-inflammatory properties of GTFs may help mitigate H. pylori-induced gastric inflammation. In this computational study, we employed molecular docking simulations using AutoDock Vina to evaluate the binding potential of key GTFs against H. pylori virulence factors CagA and VacA. EGCG exhibited a docking score of −198.72 kcal/mol against CagA, while Theaflavin-3-gallate scored −177.19 kcal/mol against VacA, indicating strong binding affinities. These in silico results suggest that GTFs, particularly EGCG, may effectively target H. pylori pathogenic proteins and impair their function. Overall, the findings support the therapeutic potential of GTFs and highlight the value of computational approaches in screening natural antibacterial compounds.