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Klebsiella pneumoniae is an opportunistic pathogen with various virulence factors that give it the capability to invade a host. Nevertheless, the treatment of bacterial infection is gradually complicated as the bacteria can develop resistance to antimicrobial agents. As nanotechnology is a prosperous field for researchers, we employed zinc oxide (ZnO) nanoparticles (NPs) on isolates of Klebsiella pneumoniae. Here, we studied the effect of three NP concentrations—0.25, 0.50, and 0.75 mM—on the gene expression of Klebsiella pneumoniae capsules in isolates collected from different samples. After conducting an anti-bacterial test, the highest nine types of bacteria that resisted the antibacterial agent were chosen for further examination. The gene expression of four genes responsible for capsule manufacturing, namely magA, k2A, rmpA, and kfu, were investigated. When the NP concentration was 0.25 mM, the lowest efficiency was obtained. However, when the concentration increased to 0.50 mM, a noticeable effect on gene expression was detected; consequently, at a concentration of 0.75 Mm, the highest impact was achieved and the gene expression was stopped.