In this study, minocycline-imprinted hydrogels are developed for controlled drug delivery in ocular disease treatments. An integrated computational and experimental study are conducted for investigating the relationship between design parameters and the drug loading/release performance of hydrogels. First, suitable functional monomers are determined for successful drug-imprinting by studying pre-polymerization conditions with full-atom molecular dynamics (MD) simulations. MD simulations suggest that acrylic acid and itaconic acid are suitable monomers for imprinting minocycline. Then, minocycline-imprinted hydrogels are synthesized with acrylic acid, commonly used in hydrogels, and three different amounts of cross-linker ethylene glycol dimethacrylate, 1, 2 and 3mol%. All hydrogels are characterized and their drug loading and release performances are determined. Our computational and experimental calculations indicate an optimum cross-linker amount of 2mol% for controlled minocycline release from imprinted hydrogels with an imprinting factor of almost 3. Finally, the drug release kinetics are determined by Korsmeyer-Peppas model.