C-phycocyanin (C-PC) is a protein-pigment widely used in nutrition and pharmaceutical applications. High purity of C-PC is a limiting factor required for its medical use; hence purity improvement with successful plausible pharmaceutical application is the state of the art of the present work. Highly purified C-PC (A 620 /A 280 = 6.6) was obtained from Thermosynechococcus elongatus. Combined enzymatic cell wall degradation, cellular exposure to high pressure, sonication, and one-time homogenization was found to be an effective purification protocol. Purified complex was confirmed by SDS-PAGE and UV-absorption spectral analysis. Cytotoxic effect of the obtained C-PC was assessed in vitro using a panel of cancer cells. Results showed that MCF-7 cells were most sensitive to C-PC (IC 50 = 158.9 µM) compared to Caco-2 (IC 50 = 258.3 µM) and HepG2 (IC 50 = 277.5 µM) cells. Our findings shed the light on the potential medical use of C-PC isolated from T. elongatus in controlling cancer cells.