Background: OqxB is an efflux pump that has emerged as a factor contributing to antibiotic resistance in Klebsiella pneumoniae. The objective of this study was to investigate the occurrence of AcrAB efflux pump resistance genes in clinical samples of K. pneumoniae and to evaluate the influence of selenium nanoparticles (Se-NPs), loaded with ampicillin, on the expression of the OqxB gene associated with efflux pumps. Methods: A total of 500 clinical samples were collected from hospitalized patients, and 60 strains of K. pneumoniae were isolated using standard microbiological methods. These strains were then analyzed using phenotypic and polymerase chain reaction (PCR) techniques to detect the frequency of KPSM, MRK, OqxA, and OqxB genes through multiplex PCR. The impact of Se-NPs loaded with ampicillin on the expression of the OqxB resistance gene was investigated using a real-time PCR technique. Results: Based on the results of this study, it was found that the KPSM gene is not present in any of the investigated K. pneumoniae isolates. However, the MRK, OqxA, and OqxB genes were detected in 57, 55, and 54 isolates, respectively. The minimum inhibitory concentration (MIC) values for Se-NP and Se-NPs with ampicillin were reported to be 1500 μg/mL and 375 μg/mL, respectively. Notably, the SeNPs with ampicillin could significantly down-regulate the expression of the OqxB gene. These findings demonstrated the potential of Se-NPs as a promising strategy for reducing antibiotic resistance in K. pneumoniae infections. Conclusion: The findings emphasize the notable prevalence of drug resistance genes, specifically those associated with efflux pump production, in clinical samples of K. pneumoniae. Remarkably, the utilization of Se nanoparticles loaded with ampicillin demonstrated its efficacy in suppressing the expression of the OqxB gene and enhancing bacterial susceptibility to ampicillin. The results further imply that Se-NPs could serve as a promising avenue for the development of innovative antibacterial agents, aimed at combating antibiotic resistance in K. pneumoniae infections.