While the pharmacology of Ginkgo biloba leaf extract has been studied extensively, little is known about the pharmacological potential of Ginkgo biloba seeds, although they contain similar active ingredients that are responsible for the therapeutic effects of the leaf extract. In this study we used 70%-methanol Ginkgo biloba kernel extract, quantified its bioactive constituents and tested their cytotoxic effect on two cancer cell lines, A2058 and HCT116, and the non-tumor cell line McCoy-Plovdiv. We studied the biological effect of the extract by real-time analysis in the xCELLigence system, WST-1 assay and LIVE/DEAD viability assay. We show that the extract significantly perturbed the viability of cancer cells in a concentration- and time-dependent manner. In contrast, non-cancerous McCoy-Plovdiv cells sustained their proliferation potential even at high concentrations of the extract. Therefore, we propose that the active constituents of the Ginkgo biloba endosperm extract may interact additively or synergistically to protect against cancer.