Helicobacter pylori (H. pylori) can be eradicated immediately while conducting an endoscopic examination. The eradication rate of intraluminal therapy for H. pylori infection (ILTHPI) is 53.7% (51/95) via local application of single-dose medicament containing amoxicillin, metronidazole, and clarithromycin. We aimed to evaluate factors affecting ILTHPI and to assess the efficacy among single antibiotics, and compared our results with combined antibiotics. We enrolled H. pylori-infected treatment-naïve symptomatic patients; 95 completed triple-antibiotic ILTHPI were evaluated for risk factors, along with 60 completed mono-antibiotic ILTHPI containing amoxicillin, clarithromycin, or metronidazole in each of the 20 patients. Univariate analysis revealed the significant influence of BMI (OR: 1.15; 95% CI: 1.03–1.27, p = 0.011) and gastric juice pH (OR: 1.35; 95% CI: 1.16–1.58, p = 0.0001). Logistic regression analysis also showed significant influence of gastric juice pH (OR: 1.30; 95% CI: 1.10–1.54, p = 0.002). The eradication rate of mono-antibiotic ILTHPI is significantly lower than triple-antibiotic ILTHPI (11.7% vs. 53.7%; p < 0.0001; α = 0.05, power = 1.0). The efficacy was 20% (4/20) for metronidazole, 10% (2/20) for amoxicillin, and 5% (1/20) for clarithromycin. In conclusion, the level of gastric juice pH is a crucial factor affecting the ILTHPI. The detection of gastric juice pH and selection of optimal intraluminal medicaments are important. Further studies with combined antibiotics for ILTHPI, perhaps metronidazole-containing medicaments, are recommended.