The association between proton-pump inhibitor (PPI) use and systemic infections caused by bacterial translocation is unclear. This study aimed to investigate whether patients receiving PPI therapy have a higher risk of bloodstream infections (BSI) without an identifiable source of infection. We conducted a hospital-based case-control study which enrolled all patients aged 20 years and older who were hospitalized in Ichinomiya Nishi Hospital with BSI confirmed by two sets of positive blood cultures in 2019. Patient data were collected from medical records, and the bacterial translocation-type (BT-type) BSI group was defined as patients with BSI without an identifiable source of infection, whereas those with a BSI from an identifiable source were assigned to the control group based on the diagnostic criteria for each infectious disease. Data from 309 patients, including 66 cases and 243 controls, were analyzed. Compared with PPI non-users, PPI users had a 2.4-fold higher risk of developing BT-type BSI after controlling for potential confounders (adjusted odds ratio: 2.41, 95% confidence interval: 1.29-4.51, P = 0.006). In conclusion, PPI use is associated with a higher risk of BSI without an identifiable source; therefore, PPI use might increase the risk of BSI secondary to bacterial translocation.