To formulate novel chitosan (CS)-coated–PLGA–nanoparticles (NPs) using a central composite design approach and use them in order to improve brain bioavailability for catechin hydrate (CH) through direct nose-to-central nervous system (CNS) delivery for the evaluation of a comparative biodistribution study of CH by the newly developed ultra high performance liquid chromatography mass spectroscopy and mass spectroscopy (UHPLC-MS/MS) method in the treatment of epilepsy. For PLGA–NPs’ preparation, a double emulsion-solvent evaporation method was used, where a four-factor, three-level central composite design was used to obtain the best nanoformulation. For the optimization, four independent variables were chosen, that is, PLGA, polyvinyl alcohol (PVA), sonication time, and temperature. The optimized PLGA–NPs were further coated with chitosan and assessed for drug release, nasal permeation study, as well as a comparative pharmacokinetic and pharmacodynamic study. Independent and dependent variables helped to optimize the best nanoformulation based on the composition of PLGA (50.0 mg), PVA (1.10%), sonication time (90.0 s), and temperature (25.0 °C). The values of dependent variables were observed, such as polydispersity index (PDI), particle size, and zeta potential (ZP)—that is, 0.106 ± 0.01, 93.46 ± 3.94 nm, and −12.63 ± 0.08 mV, respectively. The ZPs of CS-coated PLGA–NPs were changed from negative to positive value with some alteration in the distribution of particle size. Excellent mucoadhesive-nature of CS–CH–PLGA–NPs as compared with CH–S and CH–PLGA–NPs was seen, with a retention time of 0.856 min and m/z of 289.23/245.20 for CH, together with a retention time of 1.04 min and m/z of 301.21/151.21 for Quercetin as an internal standard (IS). For a linear range (1–1000 ng mL−1
), % accuracy (93.07–99.41%) and inter- and intraday % precision (0.39–4.90%) were determined. The improved Cmax
with area under curve (AUC)0–24
was found to be highly significant (p
< 0.001) in Wistar rats’ brain as compared with the i.n. and i.v. treated group based on the pharmacokinetics (PK) results. Furthermore, CS–CH–PLGA–NPs were found to be more significant (p
< 0.001) for the treatment of seizure threshold rodent models, that is, increasing current electroshock and pentylenetetrazole-induced seizures. A significant role of CS–CH–PLGA–NPs was observed, that is, p
< 0.001, for the enhancement of brain bioavailability and the treatment of epilepsy.