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Baicalin is a multi-purpose flavonoid used in the treatment of different ocular diseases. Owing to its poor stability in basic pH and its poor solubility, a suitable carrier system is needed to enhance its ocular therapeutic potential. Therefore, the objective of this work was to prepare and contrast different baicalin vesicular systems; namely liposomes, penetration enhancer vesicles PEVs and transfersomes. Results revealed that baicalin vesicles exhibited suitable particle size and zeta potential, high entrapment efficiency and controlled release. Depending on the vesicular composition, selected formulations were able to resist physical changes of particle size, zeta potential, entrapment efficiency and in vitro release after storage for 3 months, while retarding the degradation of baicalin. Selected vesicular formulations displayed equivalent or superior antioxidant potential compared to baicalin solution, with absolute superiority over ascorbic acid reference, while demonstrating sterilization endurance and safety on ocular tissues. Pharmacokinetic studies revealed that transfersomes displayed the fastest onset of action, while liposomes displayed the highest extent of absorption as concluded from the Tmax, Cmax, and AUC0-∞ values with 4–5 folds increase in bioavailability compared to baicalin control solution. This delineates baicalin vesicular systems as a promising platform for treatment of ocular diseases such as inflammation, cataract and diabetic retinopathy.