The fruits of the Sea buckthorn (Hippophae rhamnoides L.) are a popular plant food and a valuable health product. Cultivating plants produces a lot of leaves with fine branches as an unnecessary residue, which needs valorization. The aim of the study was to estimate (by HPLC-MS/MS) the qualitative and quantitative content of polyphenolic compounds in different parts of H. rhamnoides (HR), and to determine the level of antioxidant activity of leaves and fruits (by DPPH, ABTS methods and ferrozine test). Up to 19 compounds were identified in different parts of HR. The fruits are rich in flavonoids, including various glycosides of flavonols isorhamnetin, quercetin, and kaempferol. Two isorhamnetin glycosides were not identified in the leaves, while isorhamnetin-3-rhamnosylglactosides and the ellagitannins hippophaenin B, stachyurin and casuarinin were present only in the leaves of the plant. The bark and roots contained considerably more catechins, but minimal flavonols than the fruits and leaves of HR. The total phenolics and flavonols were most abundant in water infusions from leaves of HR (especially quercetin-3-O-glucoside-7-O-rhamnoside), compared to methanolic extracts. No significant differences in the quantitative and qualitative content of the fresh and dried leaves were detected. The highest antioxidant activity by all three methods was detected in the leaves of HR. In addition to the fruits, the leaves may have a perspective as a source of biologically active substances of HR.