Objective A dedicated stool container is required for Helicobacter pylori stool antigen testing. If H. pylori fecal antigen can be measured from a fecal occult blood test container (S fecal collection container or S container), which is widely used for colorectal cancer screening, screening of the upper and lower gastrointestinal tract can be performed with a single stool sample. We investigated the clinical usefulness of an H. pylori stool antigen assay using an S container. Materials A total of 347 patients who underwent esophagogastroduodenoscopy (EGD) were included. After the procedure, H. pylori stool antigen was measured using the S container and collection container recommended for H. pylori stool antigen (BL-stool collection container or BL container), and the qualitative outcomes of each were compared. A bioluminescent enzyme immunoassay (BLEIA) was used to measure H. pylori stool antigen. Results The overall agreement between S containers and BL containers was 100% (347/347), indicating that the qualitative outcomes were equivalent. As a secondary analysis, the results of the S container samples were evaluated according to the diagnosis made by physicians, and the overall agreement rate was 99.7% (345/346), indicating a high correlation. Conclusion The detection of H. pylori stool antigen using the S container is clinically useful because the results are equivalent to those obtained by the usual method. Screening of the upper and lower gastrointestinal tract is expected to be possible with a single stool sample in the future.