Helicobacter pylori infection is a prevalent gastrointestinal condition with significant public health implications, particularly among adolescents. Understanding its prevalence and associated risk factors among secondary school students is crucial for effective prevention and management strategies. This study aimed to determine the prevalence of H. pylori among secondary school students in Benin City and investigate associated risk factors. A cross-sectional study was conducted among 400 secondary school students in Benin City. Participants provided stool samples for H. pylori antigen testing and completed a questionnaire regarding demographic information, housing conditions, hygiene practices, and gastrointestinal symptoms. Data were analysed using SPSS version 22.0. The prevalence of Helicobacter pylori (H. pylori) among secondary school students in Benin City was 32% (128/400). Significant associations were found between H. pylori infection and age, housing conditions (specifically residing in rooming apartments), and handwashing after defecation (p<0.05). Gender, number of persons per room, cleanup behaviour after defecation and toilet type were not significantly associated with H. pylori prevalence (p>0.05). Symptoms such as epigastric pain and blood in stool were significantly associated with H. pylori positivity (p<0.05), while bloating and loss of appetite showed no significant association (p>0.05). In conclusion, the prevalence of H pylori among secondary school students is high, emphasising the need for targeted interventions to reduce transmission, promote hygiene practices, address associated symptoms and implement effective prevention strategies within this population.