The global burden of bacterial infection and antimicrobial resistance increases the demand to associate more than one antibiotic to fight life-threatening bacteria. Therefore, there is a great necessity to develop simple and sensitive methods for routine analysis of clinical samples. Therapeutic drug monitoring, bioequivalence, and pharmacokinetic studies are essential to ensure drug efficiency and safety. Herein, therefore, the first ecofriendly liquid chromatography −tandem mass spectrometry (LC–MS/MS) method was developed and fully validated for simultaneous determination of a commonly combined antibiotic for methicillin-resistant Staphylococcus aureus (MRSA), vancomycin (VCM) and gentamicin (GTM), in rat plasma after parenteral administration. VCM and GTM were extracted from plasma sample using acetonitrile (ACN)/0.1% TFA-induced protein precipitation followed by the separation on an Agilent Eclipse Plus ODS (3 mm × 100 mm, 3.5 μm) column using water-enriched mobile phase consisting of water containing 0.1% THF/ACN (85:15, v/v%) at flow rates of 0.30 mL min–1. The mass spectrometry parameters were optimized, and multiple reaction monitoring (MRM) in positive ion mode of two transitions was utilized for quantification of precursor to product ion at m/z 725.5 → 144 and 100.1 for VCM as [M + 2H]2+, 478.3 → 322.2 and 156.9 for GTM, and 586.3 → 162.9 and 425.3 for amikacin (AMK) internal standard, as [M + H]+. The current method has been validated as per U.S. FDA bioanalytical guidelines in terms of linearity, accuracy, precision, selectivity, recovery, matrix effects, and stability. The method was linear in the range of 1–2000 ng mL–1 and 1–1000 ng mL–1 with detection limits (S/N of 3) of 0.18 and 0.09 ng mL–1 for VCM and GTM, respectively. The selectivity and high sensitivity allow the current method to succeed in the study of pharmacokinetic parameters and drug–drug interaction between VCM and GTM after single-dose administration. VCM increased plasma clearance and elimination rate constant of GTM when coadministered and GTM also too. The change of serum chemistry analysis and significant elevation of creatinine and BUN indicate an alteration in kidney function in group III in those given the combined antibiotics. Our finding illustrated the nephrotoxicity of the two drugs when associated. The ecofriendly, simplicity, and rapidity of the current study made it a promising method for high-throughput biomonitoring in clinical samples.