This study investigates the thermodynamic and advanced nonlinear kinetic modeling of neem oil extraction using hexane as a solvent, aimed at advancing second-generation feedstock for environmental sustainability. Key process parameters—extraction temperature (32 °C to 74 °C), particle size (0.1 mm to 0.5 mm), and extraction time (0 to 180 minutes)—were systematically investigated to assess their effects on oil yield and diffusion coefficients. Six nonlinear kinetic models, including power law, parabolic diffusion, hyperbolic, Elovich, pseudo-first-order, and pseudo-second-order models were evaluated for their accuracy in describing the extraction process. The results showed that the highest oil yield of 42.9% was obtained at 74 °C, with a particle size of 0.1 mm, over 180 minutes. Diffusion coefficients increased with temperature, ranging from 2.16 × 10−12 m2/s at 32 °C to 3.89 × 10−12 m2/s at 74 °C, and decreased with larger particle sizes. The activation energy was determined to be 24.7 kJ/mol. ANOVA indicated that temperature had the most significant impact on oil yield, followed by particle size and extraction time. The parabolic diffusion and power law models provided the best fit to the experimental data, demonstrating the highest adjusted R2 and lowest RMSE and SSE values. Thermodynamic analysis revealed that the process is endothermic, spontaneous, and irreversible, with entropy, enthalpy, and Gibbs free energy values of 0.10 kJ/mol⋅K, 31.9 kJ/mol, and −2.08 kJ/mol, respectively, at 328 K. These findings provide critical insights for optimizing neem oil extraction, supporting its industrial application as a sustainable feedstock.