Waste solid residue from the hydrothermal extraction of pectin derived from sugar beet pulp was used as feedstock in the production of 5-hydroxymethylfurfural (5-HMF). The depolymerization of pectin-free sugar beet pulp (PF-SBP) to monosaccharides and their dehydration to 5-HMF were conducted in subcritical water using a batch reactor. The experimental design methodology was used in order to model the hydrothermal process and to optimize the operational parameters of the reaction, namely temperature and holding time. These parameters are required to achieve the highest yield of 5-HMF. The model predicts, in good agreement with experimental results (R2 = 0.935), an optimal yield of 5-HMF (of approximately 38% in relation to the cellulosic fraction content in the PF-SBP) at a temperature of 192.5 °C and a holding time of about 51.2 min. 5-HMF was successfully isolated from the reaction mixture using the liquid–liquid extraction method. The results are suitable for industrial upscaling and may become an incentive to introduce a new, environmentally friendly, uncomplicated, and efficient waste treatment method. The method would be used to treat products from the sugar refining industry, the treatment of which has proven to be problematic until now.