Thymol is a monoterpene phenolic derivative extracted from the Thymus vulgaris which has antimicrobial effects. In the present study, thymol-loaded chitosan nanogels were prepared and their physicochemical properties were characterized. The encapsulation efficiency of thymol into chitosan and its stability were determined. The in vitro antimicrobial and anti-biofilm activities of thymol-loaded chitosan nanogel (Ty-CsNG), free thymol (Ty), and free chitosan nanogel (CsNG) were evaluated against both Gram-negative and Grampositive multidrug-resistant (MDR) bacteria including Staphylococcus aureus, Acinetobacter baumanii, and Pseudomonas aeruginosa strains using the broth microdilution and crystal violet assay, respectively. After treatment of MDR strains with sub-minimum inhibitory concentration (Sub-MIC) of Ty-CsNG, free Ty and CsNG, biofilm gene expression analysis was studied. Moreover, cytotoxicity of Ty-CsNG, free Ty, and CsNG against HEK-293 normal cell line was determined using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) method. The average size of Ty-CsNG was 82.71 � 9.6 nm, encapsulation efficiency was 76.54 � 0.62 % with stability up to 60 days at 4 °C. Antibacterial activity test revealed that Ty-CsNG reduced the MIC by 4 -6 times in comparison to free thymol. In addition, the expression of biofilm-related genes including ompA, and pgaB were significantly down-regulated after treatment of strains with Ty-CsNG (P < 0.05). In addition, free CsNG displayed negligible cytotoxicity against HEK-293 normal cell lines and presented a biocompatible nanoscale delivery system. Based on the results, it can be concluded that Ty-CsNG can be considered a promising candidate for enhancing antimicrobial and anti-biofilm activities.