The role of efflux pumps in antibiotic resistance development among Escherichia coli may have been underappreciated. The objective of this study was assessment the association of AcrAB-TolC efflux pumps and qepA genes with resistance to common antibiotics among E. coli isolates. A total of 200 E. coli isolates were obtained from diverse samples of inpatients. Minimum inhibitory concentrations and Kirby–Bauer disk diffusion tests were determined for ceftazidime, cefotaxime, imipenem, gentamicin, and tetracycline. The Acr-AB-TolC and qepA genes were amplified using PCR technique and their association with antibiotics was also evaluated using Chi-square test. A majority of isolates (64%) were retrieved from gastrointestinal samples, followed by urinary tract infections (33%), and bloodstream (3%). All the isolates were resistant to ampicillin (100%), followed by cefazolin (59%), and cefoxitin (58%). However, 100% of the isolates showed susceptibility to fosfomycin. The prevalence of acrA, acrB, and qepA genes was 94% (n = 188), 86% (n = 172), and 8% (n = 16), respectively. The acrA and acrB were significantly associated with resistance to cefoxitin and cefazolin (P < 0.01), ceftazidime (P < 0.01), carbapenems (P = 0.022), and tetracycline (P = 0.0112). In addition, qepA gene was significantly associated with tetracycline resistance (P = 0.032). None of the patients had death outcome. A majority of E. coli isolates harbored the AcrAB genes, but qepA was observed among lower number of the isolates. It is notable that three strains lacked the extended spectrum beta-lactamase and carbapenemases and none of multidrug resistant strains carried tet and aminoglycoside modifying enzymes genes. Over-expression of efflux pumps has been increasingly is associated with clinically relevant antibiotic resistance. For this reason, the expression and functionality of efflux pumps should be more investigated profoundly and be compared between drug-resistant and drug-susceptible isolates.