The purpose of this study is to shed light on the phenolics content and the presence of different classes of constituents in the flowers, leaves, and stems of Sambucus nigra L. cultivated in Egypt along with screening out their cytotoxic activity. Colorimetric investigation revealed that all tested samples were rich in phenolics. HPLC qualitative analysis revealed the presence of different phenolics including chlorogenic acid and rutin that were isolated and identified using 1H and 13C NMR. The ethanolic extracts of the three organs, together with the two isolated phenolics, were tested for their cytotoxic activity against hepatocellular carcinoma, human lung adenocarcinoma, and human colon carcinoma. All tested samples were able to reduce the viability of the tested cell lines in a dose-response manner comparable to staurosporine as a reference drug. Molecular docking studies were performed for chlorogenic acid and rutin. Their ability to interact with the key amino acids in B-cell lymphoma 2 (Bcl-2) protein binding site rationalizes their pronouncing activity as proven by its docking pattern and docking score. The cytotoxic activity of the flowers, leaves, and stems of Sambucus nigra L. has been attributed to the synergetic effects of phenolic compounds, which affords the basis for investigations as promising candidates for discovering new anticancer drugs.