Objective: To explore the effects and pharmacoeconomic value of sequential therapy and standard triple therapy in eradication of Helicobacter pylori (Hp) infection in children. Methods: A total of 90 children with Hp infection (aged 4–14 years) were randomly divided into group I and group II, with 45 cases in each group. Effectiveness and economic benefits of Hp eradication in the two groups of children were specially compared and analyzed. Results: Forty-two cases in group I and 43 cases in group II completed treatment and review respectively. According to intention to treat (ITT) and per protocol (PP), Hp eradication rates in group II were 86.67% and 90.70%, which were higher than 66.67% and 71.43% in group I (P<0.05). After treatment, the clinical symptom scores of Hp infection in the two groups decreased significantly, and the scores of “abdominal distension” and “anorexia” in group II were lower than those in group I (P<0.05). There was no significant difference in the incidence of adverse reactions and recurrence rate after 12 months of follow-up between the two groups (P>0.05). The treatment cost of group II was (356.83±42.06) yuan, which was lower than that of group I (457.08±55.19) yuan. According to ITT and PP analysis, the cost/effectiveness (C/E) of group II was 411.70 and 393.42, which were lower than that of group I (685.59 and 639.90). Conclusion: the eradication rate of sequential therapy for children with Hp infection is higher than that of standard triple therapy, with good safety, and the cost of treatment and C/E are significantly reduced, and the value of pharmacoeconomic is remarkable.