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The vast spread of multidrug-resistant bacteria has encouraged researchers to explore new antimicrobial compounds. This study aimed to investigate the phytochemistry and antibacterial activity of <i>Cycas thouarsii</i> R.Br. leaves extract against <i>Klebsiella pneumoniae</i> clinical isolates. The minimum inhibitory concentration (MIC) values of <i>C. thouarsii</i> extract ranged from 4 to 32 µg/mL. The impact of the treatment of the isolates with sub-inhibitory concentrations of <i>C. thouarsii</i> extract was investigated on the bacterial growth, membrane integrity, inner and outer membrane permeability, membrane depolarization, and bacterial morphology using a scanning electron microscope (SEM) and on the efflux activity using qRT-PCR. Interestingly, most <i>K. pneumoniae</i> isolates treated with <i>C. thouarsii</i> extract showed growth inhibition—a decrease in membrane integrity. In addition, we observed various morphological changes, a significant increase in inner and outer membrane permeability, a non-significant change in membrane depolarization, and a decrease in efflux activity after treatment. The phytochemical investigation of <i>C. thouarsii</i> extract revealed the isolation of one new biflavonoid, 5,7,7″,4‴-tetra-<i>O</i>-methyl-hinokiflavone (<b>3</b>), and five known compounds, stigmasterol (<b>1</b>), naringenin (<b>2</b>), 2,3-dihydrobilobetin (<b>4</b>), 4′,4‴-<i>O-</i>dimethyl amentoflavone (<b>5</b>), and hinokiflavone (<b>6</b>), for the first time. Moreover, the pure compounds′ MICs′ ranged from 0.25 to 2 µg/mL. Thus, <i>C. thouarsii</i> could be a potential source for new antimicrobials.