A newly UHPLC-MS/MS method development and validation for S-Allyl Cysteine was used to evaluate the comparative pharmacokinetic parameters. SC PLGA NPs (S-Allyl Cysteine Poly (D,L-lactide-co-glycolic acid) Nanoparticles) were developed by the emulsion solvent evaporation method. SC PLGA NPs showed their drug loading and encapsulation efficiency to be 5.13 ± 0.10% and 82.36 ± 4.01%, respectively. SC PLGA NPs showed a spherical morphology of an average size (134.8 ± 4.61 nm), PDI: 0.277 ± 0.004, and −25.3 ± 1.03 mV Zeta-Potential (ZP), and is suitable for oral delivery. The development and validation of the UHPLC-MS/MS bioanalytical method were performed successfully for PK-parameter examinations with 1.219 min RT, MS (162.00/73.10), and a total run-time of 2.0 min. Additionally, 1.0–1000.0 ng/mL was a linear range with inter- and intra-day accuracy of 92.55–99.40%, followed by a precision of 1.88–4.23%. SC PLGA NP’s oral bioavailability was significantly higher (** p p < 0.01) in comparison to SC-S. SC PLGA NPs showed fitted physicochemical and enhanced antimicrobial properties, which can be helpful for oral administration. Based on the proposed research results, SC PLGA NPs were used for the improvement in oral bioavailability with a sustained and controlled release of S-Allyl-L-Cysteine delivery.