Cucumber is an important agricultural crop that is cultivated under greenhouse conditions. Cucumber cultivation generates substantial quantities of green waste that require proper disposal. The lack of data on the chemical composition of cucumber greens and their biological activity emphasizes the necessity for research on useful products resulting from this widely available waste. Our examination of the flavonoid contents in the leaves and stems of 30 cucumber cultivars revealed 6 cultivars with high flavonoid contents. In addition, the cutting time did not cause negative effects, and we observed a positive effect with 0.05–0.10% organomineral fertilizer application on the flavonoid levels in the greens. Liquid chromatography–mass spectrometry detected 38 apigenin derivatives, including acylated and non-acylated cucumerins and C-, O-, and C,O-glycosides. Among these, 12 known flavonoids and 18 novel compounds were identified. The concentrations of these compounds in the six flavonoid extracts varied at 39.85–181.53 mg/g for the non-acylated flavones, 14.67–293.31 mg/g for the cucumerins, and 401.73–892.17 mg/g for the acylated flavones. Oral administration of the total flavonoid extracts (at a dosage of 100 g/kg/day) resulted in a hypolipidemic effect in hyperlipidemic hamsters, with subsequent normalization of their serum lipid profiles, malondialdehyde levels, and liver antioxidative enzyme activities. These results substantiate the lipid-lowering potential of cucumber waste extracts. Our investigation of the selected flavonoid activity showed that isovitexin-2′′-O-glucoside-6′′-O-p-coumarate (administered at 50 g/kg/day) had the highest hypolipidemic potency. These results can contribute to the practical use of cucumber green waste and the development of novel supplements for diseases linked to high-fat consumption.