Walnut byproducts have been shown to exert functional properties, but the literature on their bioactive content is still scarce. Among walnut byproducts, walnut septum is a dry ligneous diaphragm tissue that divides the two halves of the kernel, exhibiting nutritional and medicinal properties. These functional properties are owing to its flavonoid content, and in order to explore the flavonoid fraction, an ultrasound-assisted (UAE) protocol was combined with solid phase extraction (SPE) and coupled to high-performance liquid chromatography with diode array detection (HPLC-DAD) for the determination of flavonoids in Greek walnut septa membranes belonging to Chandler, Vina, and Franquette varieties. The proposed UAE-SPE-HPLC-DAD method was validated and the relative standard deviations (RSD%) of the within-day and between-day assays were lower than 6.2 and 8.5, respectively, showing good precision, and high accuracy ranging from 90.8 (apigenin) to 97.5% (catechin) for within-day assay, and from 88.5 (myricetin) to 96.2% (catechin) for between-day assay. Overall, seven flavonoids were determined (catechin, rutin, myricetin, luteolin, quercetin, apigenin, and kaempferol) suggesting that the walnut septum is a rich source of bioactive constituents. The quantification results were further processed using ANOVA analysis to examine if there are statistically significant differences between the concentration of each flavonoid and the variety of the walnut septum.