Background: The management of Helicobacter pylori (H. pylori) infection raises important challenges, still being the most common chronic infection worldwide in all age groups. In high-prevalence regions, paediatric patients need a specific focus, as the acquisition of the infection takes place in childhood. The objective of this study was to analyze the endoscopic and histopathologic changes of the gastric mucosa in H. pylori infected children. Material and Methods: A retrospective study was performed on consecutive paediatric patients, ranging from 0 to 18 years of age, who underwent an upper gastrointestinal endoscopy (UGE) for a period of 5 years, regardless of their symptomatology. Endoscopy reports and histological slides were reviewed and clinical, endoscopic, and histologic data were recorded. Results: A total of 248 patients were included in the study, 82 (33.06%) of them being H. pylori infected. There was no difference in age and symptoms between the infected and noninfected group. A significant association was found between the H. pylori infection and histopathological parameters such as acute and chronic inflammatory infiltrate. The bacterial load influences the intensity of inflammation (p < 0.001). The chronic inflammation was predominant, only 23.2% of the patients displayed acute inflammation (p < 0.0001). The topographic distribution of inflammation was dominated by pangastritis (p = 0.04) with 58.6% of the patients presenting similar degrees of inflammation both in the antrum and corpus. Conclusion: Endoscopic features such as nodularity of the antral mucosa (p < 0.05) along with histological findings as lymphoid follicles (p < 0.05) are suggestive of H. pylori infection. However, the concordance between the endoscopic and histological diagnosis is still far from perfect (Cohen’s k coefficient = 0.42), maintaining the need for an invasive approach in children.