This study evaluates the in vivo mucoadhesive properties of thiolated cyclodextrins (CDs) with varying S-protection using polyethylene glycol (PEG) of different chain lengths. Free thiol groups of thiolated β-CDs (CD-SH) were S-protected with 1 kDa and 2 kDa PEG bearing a terminal thiol group, leading to third-generation of thiolated CDs (CD-SS-PEG). The structure of these thiolated CDs was confirmed and characterized by FT-IR, 1 H NMR, and colorimetric assays. Thiolated and S-protected CDs were evaluated regarding viscosity, cellular uptake and, in vitro and in vivo mucoadhesion. The viscosity of CD-SH, CD-SS-PEG 1 kDa, and CD-SS-PEG 2 kDa mixtures with mucus increased 9-, 7-, and 5.5-fold, respectively, compared to unmodified CD within 3 h. Cellular uptake on Caco-2 cells was 1.75 times higher for highly thiolated CDs than for unmodified CD. In vitro residence time on porcine intestine was prolonged 7-, 8.4-, and 7.9-fold for CD-SH, CD-SS-PEG 1 kDa, and CD-SS-PEG 2 kDa, respectively. In vivo results indicated CD-SS-PEG 1 kDa had the highest potential. Our comprehensive in vitro, ex vivo, and in vivo ffindings demonstrate that CD-SS-PEG 1 kDa is a highly promising candidate for mucoadhesive drug delivery systems.