Egyptian kaolinite was applied in the synthesis of zeolite-A by conventional hydrothermal and alkali fusion methods, resulting in two forms of zeolite-A: the hydrated phase (H.ZA) and the dehydrated phase (DH.ZA). The DH.ZA phase exhibits an enhanced surface area (488 m2/g), total basicity (7.73 mmol OH/g), high sodium content (20.2%), and a narrow particle size distribution (5 to 25 µm) as compared to the H.ZA phase (423 m2/g surface area, 5.88 mmol OH/g total basicity, 13.3% sodium content, and 10 to 45 µm particle size distribution). DH.ZA exhibits enhanced catalytic activity, achieving a biodiesel yield of 96.8% after 60 min at 60 °C, while the application of H.ZA resulted in a 95.8% yield after 120 min at 80 °C. The controlled transesterification mechanism in the presence of H.ZA and DH.ZA involved robust base-catalyzed reactions. The reactions follow the pseudo-first-order kinetics, and the rate constants (Kc) were determined at three different temperature values (40, 50 and 60 °C). The activation energies using H.ZA (35.9 kJ.mol−1) and DH.ZA (32.714 kJ.mol−1) demonstrates their efficiencies in mild conditions. The thermodynamic parameters of enthalpy (33.23 kJ.mol−1 (H.ZA) and 30.03 kJ.mol−1 (DH.ZA)), Gibb’s free energy (65.164 kJ.mol−1 (H.ZA) and 65.268 kJ.mol−1 (DH.ZA)), and entropy (−195.59 J.K−1.mol−1 (H.ZA) and −195.91 J.K−1.mol−1 (DH.ZA)) demonstrate the spontaneous and endothermic behaviours of these reactions. The obtained biodiesel matches the physical properties of the international standards, and the recyclability properties of the two zeolite phases demonstrate their suitability for commercial-scale applications.