The rise in drug resistance poses escalating challenges for antibacterial medications, leading to an urgent demand for the exploration and innovation of new antibacterial drugs. Fagraea fragrans Roxb., belonging to the Gentianaceae family, is one of the common herbal medicines which can be found abundantly in Southeast Asia. The secoiridoid glucoside swertiamarin, one of the major compounds in F. fragrans leaf, exhibits antimicrobial effects. To guarantee the medicinal effectiveness of F. fragrans leaves, it is essential to identify a standardized analytical method for quantifying the active compound. In this study, the optimized HPLC method following ICH guideline was validated for the quantitative analysis of swertiamarin content in F. fragrans leaf in terms of linearity (y = 5733.5x - 369.1; R2 = 0.9999), accuracy (93.57-96.39% recovery), precision (0.91% RSD for repeatability precision; 1.19% RSD for intermediate precision), limit of detection (0.73 µg/mL), limit of quantitation (2.23 µg/mL), specificity (peak purity index = 0.999995) and robustness (% RSD <1).The maximum wavelength of swertiamarin was found to be at 238 nm. The amount of swertiamarin content in F. fragrans leaf extract conducted from the validated HPLC method was found to be 0.0259 ± 0.0005 g/100 g crude drug. The leaf extract exhibited antimicrobial activity against clinical isolates of Enterobacter cloacae, Klebsiella pneumonia, and Escherichia coli at 0.125 mg/mL, and Pseudomonas aeruginosa at 0.5, showing minimum inhibitory concentration (MIC) values. Whereas swertiamarin exhibited even lower MIC values. The developed HPLC analysis effectively determines swertiamarin content as a chemical marker to ensure the antimicrobial potential of F. fragrans leaves.