The current study presents a comprehensive pharmaceutical engineering approach to developing an advanced transdermal drug delivery system for addressing skin hyperpigmentation through innovative nanocomposite gel formulation. Utilizing a systematic Quality-by-Design (QbD) methodology with Box-Behnken design, we developed a novel fluocinolone-loaded chitosan-graphene oxide nanocomposite (FCGN1) aimed at optimizing pharmaceutical performance and therapeutic efficacy. The nanocomposite formulation demonstrated critical pharmaceutical quality attributes: a precisely controlled nanoscale particle size of 144.78 ± 0.15 nm, stable zeta potential of -17.93 ± 3.75 mV, and high drug entrapment efficiency of 81.3 ± 3.64%. The optimized gel formulation (FNTG3) exhibited superior transdermal delivery characteristics, achieving approximately 70% permeation within 15 h and a significant flux rate of 190 µg/cm2, which substantially outperforms current market alternatives. The comprehensive pharmaceutical evaluation included rigorous stability studies over 45 days, confirming consistent physical stability and sustained drug permeation. In vivo assessments using a UVB-induced hyperpigmentation rat model validated the formulation's dermal tolerability and depigmentation potential, demonstrating comparable or superior performance to commercial hydroquinone treatments. Histopathological analyses revealed pronounced depigmentation effects, attributable to the synergistic design of the nanocomposite system. The strategic integration of fluocinolone, chitosan, and graphene oxide facilitated enhanced drug release kinetics and improved skin penetration, highlighting the potential of rational pharmaceutical design in developing advanced topical delivery systems. This research provides a robust framework for developing sophisticated pharmaceutical dosage forms with enhanced therapeutic performance, offering significant insights into nanoscale drug delivery technologies for dermatological applications. The findings underscore the importance of systematic optimization and multifunctional component design in creating innovative pharmaceutical formulations.