Mulberry (Morus alba L.) fruit (MF) is a rich source of functional compounds, such as anthocyanin. However, during solvent extraction, these compounds are not fully dispersed into the substrate, leading to incomplete extraction. Moreover, raw MF rapidly ripens and deteriorates after harvesting; hence, innovative methods to process MF are needed. Here, a pectinase-assisted extraction method is developed to liberate polyphenols and anthocyanins from cell wall matrices in MF. We optimized the procedure to maximize water solubility index (WSI), total phenolic (TP) content, and total anthocyanin (TA) content using a central composite design to perform a response surface methodology (RSM) analysis. The optimal conditions predicted by the RSM were a 1:5 w/v material/water ratio with 3.5% pectinase (v/w) and 1.5% citric acid (w/w) for 113 min at 50 • C. Under these conditions, the WSI, TP, and TA were significantly higher compared with those in the untreated control. The results well matched (within 5% differences) with the predicted RSM values. Furthermore, metabolite analysis revealed that the levels of cyanidin-3-O-glucoside, delphinidin hexoside, and quercetin were higher in pectinase-assisted MF extraction compared with the untreated control. This work demonstrated that pectinase-assisted extraction using citric acid could be an efficient technique to enhance the value of MF and its potential applications in the food industry. Practical Application: A pectinase-assisted extraction method was optimized to enhance the WSI, TP, and TA yields from MF extracts. The optimal conditions were predicted to be 1:5 w/v material/water ratio, 3.5% pectinase (v/w), and 1.5% CA (w/w) with a 113 min reaction time at 50 • C. Under these conditions, WSI, TP, and TA were significantly increased compared with the untreated control. These results suggested the potential of mulberry plants for use in the food industry via the development of a simple, efficient process to extract functional compounds from MF.