Cyclodextrins have a wide range of applications in different areas of drug delivery and pharmaceutical industry due to their complexation ability and other versatile characteristics. Here we have studied the binding interactions of a small biologically important phenolic molecule, Thymol (Th), with both α and β cyclodextrins (CDs), which are well known drug delivery vehicles. Extent of encapsulation has been determined using several spectroscopic techniques. In fluorescence experiments, significant increase in fluorescence intensities have been discerned for both the CDs but there had been a much early saturation for αCD. Anisotropy experiments have been performed too and very surprisingly no appreciable increase in anisotropy value was observed in either case. Isothermal titration calorimetry (ITC) data, however, show signature of binding of Th with the βCD. These intriguing results were explained with the help of molecular docking and dynamics simulation studies. The docking calculations have shown that Th goes inside both α and βCD. In keeping with the final NMR data and molecular dynamics we have ultimately concluded that solvated Th molecules are the main participants in the interaction with CDs which is responsible for these intriguing behaviors. Finally we have also performed an antioxidant assay to reveal the practical application of such encapsulation. It has been found that on encapsulation there is an enhancement of the antioxidant behavior of Th. Then we have also performed an antibacterial assay to show the unchanged antibacterial properties of Th on encapsulation. Hence it can be deduced that Th can be safely delivered through CDs in living system without hampering its beneficial properties. © 2018 Elsevier B.V.