Clinopodium vulgare L. is a valuable medicinal plant with various beneficial effects on health. In this study, water extracts from the aerial part of the wild and in vitro cultured C. vulgare plants were obtained. The polyphenol, flavonoid content and antioxidant activity of the extracts as well as their antitumor efficiency against a panel of cell lines were analyzed. The ability of C. vulgare to inhibit cancer cell migration and induce apoptosis in the tumor cells was examined by wound healing assay and fluorescence microscopic methods. The effect of the extracts on the cell cycle progression of the tumor cells was analyzed by flow cytometry. The presented results show that the antitumor activity of the extracts from in vitro cultured plants was similar to and even exceeded that of the wild plants. The cell viability and migration assays demonstrate the selective anticancer effect of the extract and significant inhibition of cancer cell proliferation and motility. The fluorescence microscopy and cell cycle analyses indicate that the antitumor activity of the in vitro plant extract was related to both antiproliferative and proapoptotic effects. These results show that C. vulgare plants obtained by in vitro micropropagation and cultivated ex vitro are promising candidates for anticancer drug therapy.