Background: Overexpression of Acr AB and Oxq AB efflux pump genes in Klebsiella pneumoniae could increase its resistance to antimicrobials. Objectives: to explore the prevalence of Acr AB and Oxq AB efflux pump genes in resistant isolates of K. pneumoniae and to detect their role in conferring the resistance to ciprofloxacin. Methodology: Isolation of K. pneumoniae was followed by detection of its antimicrobial susceptibility. Then, the ciprofloxacin minimum inhibitory concentrations (MIC) were analyzed by broth microdilution method before and after treatment with the efflux pump inhibitor, carbonyl cyanide 3-chlorophenylhydrazone. The presence of Acr AB and Oxq AB efflux pump genes was investigated by polymerase chain reaction. Results: One hundred K. pneumonia strains were isolated and 65 % of these isolates were multidrug-resistant with high resistance for sulphamethoxazole (77%), amikacin (66%), and ciprofloxacin (63%). 60.3% of ciprofloxacin-resistant K. pneumoniae had a significant 4-fold decrease or more reduction in MIC for ciprofloxacin after CCCP addition (p value<0.05). There was a significant difference concerning the frequency of efflux pump genes in ciprofloxacin-resistant isolates as 82.5% were positive and acrA, acrB, oqxA, and oqxB were detected in 77.7, 71.4, 62 and 65% of isolates, respectively. Conclusion: Acr AB and Oxq AB efflux pump genes were prevalent among K. pneumoniae isolates and they had an essential role in explaining their resistance to ciprofloxacin.