Xylooligosaccharides (XOS) obtained from lignocellulosic biomass after autohydrolysis primarily consist of ligninderived impurities and autogenerated inhibitors like furfural, hydroxymethylfurfural, and acetic acid. In this study, graphene oxide-mediated purification (GOMP), a novel and environmentally friendly downstream processing method, was developed for the purification of XOS from hydrolysate obtained after ozone-assisted autohydrolysis of wheat bran. GOMP resulted in appreciable recovery of total XOS from the hydrolysate (73.87 ± 4.25%, DP2− 6) with near complete removal of autogenerated inhibitors (furfural 85.42%, HMF 87.38%, and acetic acid 84.0%). Recovery of XOS by GOMP was higher than the conventional membrane purification technique (44.07 ± 0.92%) and activated charcoal treatment (72.76 ± 0.84%) along with comparatively higher removal of inhibitor compounds. GOMP results in the selective adsorption of inhibitors on the graphene oxide matrix from the XOS-rich hydrolysate, resulting in its purification and concentration. The prebiotic function of the obtained XOS fractions (DP2−4.48%, DP3−39.69%, DP4−36.13%, DP5−8.38%, and DP6−13.10%) was evaluated, indicating the growth stimulation of tested probiotic cultures and differential utilization of XOS oligomers DP3 and DP4 and complete consumption of DP2, DP5, and DP6 along with short-chain fatty acids as a major fermentation product. These findings suggest that GOMP, which employs a common substance (i.e., graphene oxide) used in water treatment, exhibits potential as an efficient and economically viable single-step methodology for XOS purification.