Background: Klebsiella pneumoniae shows varying degrees of resistance to antibiotic treatment; this resistance arises from multiple mechanisms, including the increased expression of multidrug (MDR) efflux pumps. An efflux pump inhibitor (EPI) is required to overcome this challenge and restore the effectiveness of antibiotics against the present MDR K. pneumoniae. Objective: To investigate the synergistic effect of the EPI Phenylalanine-Arginine β-Naphthylamide (PaβN) and Ciprofloxacin (CIP) on the expression of efflux pump genes AcrAB-TolC, isolated from CIP-resistant K. pneumoniae. Methods: 50 isolates of K. pneumoniae were collected from five different hospitals in Baghdad, Iraq. The minimum inhibitory concentration (MIC) values were determined for the CIP and CIP and PaßN combination using the broth micro-dilution method conducted on ten isolates resistant to CIP. Moreover, the expression level of AcrA, AcrB, and TolC genes from four selected isolates of K. pneumoniae were measured using quantitative real-time polymerase chain reaction (qRT-PCR). Results: K. pneumoniae isolates showed that 40/50 (80%) were multidrug-resistant, and 54% of isolates were resistant to CIP. The MIC was reduced significantly from 2–8-fold in the isolates treated with PaβN and CIP compared to the CIP-treated group. The gene expression levels varied among the four selected isolates, with a slight decrease in AcrAB-TolC gene expression in some isolates treated with the CIP and PaβN combination compared to those treated with CIP alone. Conclusions: The promising finding is the effectiveness of synergistic combinations between the antibiotic and efflux pump inhibitors in eliminating resistance of MDR bacteria.