The chiral separation of hydroxychloroquine, an antimalarial drug with one chiral center, has been predicted using molecular docking and was proven using the HPLC method. Docking utilized the PM3 semi-empirical method with specific grid coordinates (X = 19.977, Y = 20.069, and Z = 25.901) and a grid size of (X = 20, Y = 20, and Z = 60), employing a grid spacing of 1,000 Å, an exhaustiveness value of 8, and num_modes of 10. The analysis revealed the enhanced stability of R-hydroxychloroquine within the tris amylose complex, resulting in slower retention and elution rates compared to S-hydroxychloroquine. The HPLC experimental validation demonstrates resolution (Rs = 2.23), successfully achieved by employing amylose tris-based chiral columns. The mobile phase composition employed in this study consisted of acetonitrile:aquabidest: dimethylamine (47:52:1, v/v). Detection was performed at 343 nm, and the optimized HPLC method successfully quantitatively determined hydroxychloroquine in a liquid pharmaceutical sample with a percentage recovery of 98.47%.