Abstract Forming complexes with β-cyclodextrin can enhance stability, dissolution rate, solubility, and bioavailability of an active pharmaceutical ingredient. In this study, the inclusion behavior between β-cyclodextrin (β-CD) and diphenhydramine, clonidine, and tolperisone in DMSO-d6 was investigated using NMR spectroscopy. 1H, 13C, COSY, HMQC, and ROESY data were applied to determine the structure of inclusion complexes, and molecular docking analysis was engaged to identify the most favorable host–guest interactions in the inclusion complexes. Complexation of β-CD with diphenhydramine, clonidine, and tolperisone is accompanied by the insertion of a molecular fragment of the guest molecule, one molecule of diphenhydramine and tolperisone, and two molecules of clonidine, into the inner sphere of one host molecule. The reported study provides useful information for the potential application of the complexation of β-CD with diphenhydramine, clonidine, and tolperisone. This may be a good strategy for the development of solid pharmaceutical dosage forms based on β-CDs as a drug delivery system. Article highlights The inclusion complexes of β-CD and diphenhydramine, clonidine, and tolperisone were synthesized and analyzed using 1Н, 13С, COSY, HMQC, and ROESY spectroscopy. Diphenhydramine, clonidine, and tolperisone interact with β-CD with the formation of stable 1:1 stoichiometric complexes for β-CD:diphenhydramine and β-CD:tolperisone, and 1:2 stoichiometric complex for β-CD:clonidine. Possible structures of the inclusion complexes between β-CD and diphenhydramine, clonidine, and tolperisone were determined using molecular docking in the software AutoDock 4.0.