Introduction: This paper aimed to investigate, for the first time, the possibility of increasing the antibacterial activities of thymol (TH) by developing an encapsulating agent based on chitosan-grafted cyclodextrin. For this purpose, β-cyclodextrin was monosubstituted at position 6 via propargyl bromide, and chitosan’s amine groups were converted to azide functions. After alkylation and diazotization reactions, the grafting of β-cyclodextrin onto the chitosan (CSβCD) was realized via click chemistry alkyne–azide cycloaddition. Methods: The incorporation of TH into chitosan-grafted β-cyclodextrin (TH/CS-βCD) was performed by the freeze-drying method, and the encapsulation efficiency was investigated based on various mass ratios (TH:CS-βCD). The optimized inclusion complex was then thoroughly examined by scanning electron microscopy (SEM), X-ray diffraction (XRD), thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC). Results: The antibacterial activity was assessed against Escherichia coli, Staphylococcus aureus, and Bacillus subtilis using broth-microdilution assay. Fourier transform infrared spectroscopy analysis demonstrated the successful grafting of β-cyclodextrin onto chitosan since the optimum mass ratio between TH and CS-βCD was 1:8 (w:w), corresponding to 78 ± 3.42% of encapsulation efficiency, while SEM, XRD, TGA and DSC confirmed the establishment of TH/CS-βCD inclusion complexes. Conclusion: The in vitro investigation showed that TH/CS-βCD exhibited higher antibacterial properties compared to TH in free form.