Recently, there has been a burgeoning interest in harnessing the potential of biomass and industry byproducts for the development of novel products and materials. In particular, this study explored the efficient valorization of sunflower meal (SFM), an underutilized byproduct of the oil extraction industry, usually discarded or used as low-value animal feed through enzyme-aided fractionation, specifically targeting the extraction and conversion of its abundant carbohydrate component, xylan, into emerging prebiotic compounds—xylo-oligosaccharides (XOSs)—which are recognized as promotors of a healthy gut microbiome and overall human wellbeing. An enzymatic treatment using Alcalase® 2.4 L was implemented for facilitating the recovery of a highly pure hemicellulosic fraction (92.2% carbohydrates) rich in β-(1→4)-linked xylose residues with arabinose and glucuronic acid substitutions (DP-xylan). A further enzymatic treatment of this substrate, using ROHALASE® SEP-VISCO under optimized conditions (70 °C, pH 6, 0.005% v/v enzyme concentration), produced 52.3% of XOSs with a polymerization degree (DP) less than 20 after two hours. Further analyses demonstrated that the majority of the obtained product had a DP less than 6, predominantly consisting of di- and trisaccharides (XOS2 and XOS3) without the significant generation of xylose. These findings highlight the significant potential of SFM for the generation of valuable prebiotic compounds in a sustainable manner.