Klebsiella pneumoniae (K. pneumonia (is a key pathogen that can cause pneumonia, severe catheter-associated pneumoniae, respiratory failure, and other infections, particularly in immunocompromised individuals. Multidrug-resistant (MDR) K. pneumoniae has become more common due to overuse of antibiotics that led to a major threat to public health. The current study aimed to determine the resistance profile of K. pneumoniae causing respiratory tract infections (RTI) and to detect the frequency of carbapenem resistance encoding genes by PCR, along with the determination of antibacterial activity of thyme (TEO) and marjoram essential oils (MEO) on the MDR K. pneumoniae isolates. The antibiotic susceptibility patterns of the K. pneumoniae isolates were determined using the Kirby Bauer disc diffusion agar method. The frequency of carbapenem resistance encoding genes including (blaKPC, blaOXA, blaIMP, blaNDM, and blaVIM) was determined using PCR. The antimicrobial activity of TEO and MEO was assessed by determination of their minimum inhibitory concentration (MIC). Phenotypic detection of the resistance profile of 19 K. pneumoniae isolates causing RTI revealed that 100% of isolates were MDR. The frequency of carbapenem resistance encoding genes was as follows; blaNDM (100%), blaOXA (94.7%), and blaIMP (31.6%), while the frequency of blaVIM, and blaKPC was 21% and 5.26%. MEO showed higher antimicrobial activity than TEO. MIC of MEO was 0.244 µL/mL for 10.5% of MDR K. pneumoniae isolates while MIC of TEO was 3.9 µL/mL for 5.3% of isolates.