Biomedical applications of zirconia nanomaterials were limited in biological systems. In this research, 8–15 nm size zirconia nanoflakes (ZrNFs) were fabricated and their nature, morphology, and biocompatibility were evaluated. The synthesis was carried out using Enicostemma littorale plant extract as an effective reducing and capping agent. Physiochemical properties of prepared ZrNFs were characterized using diverse instrumental studies such as UV‐vis spectrophotometer, Fourier‐transform infrared, powder X‐ray diffractometer, scanning electron microscope, transmission electron microscope (TEM), energy dispersive X‐ray, and cyclic voltammetry (CV). The XRD pattern confirmed the tetragonal phases of ZrNFs and the highest crystallite size of Zr0.02, Zr0.02, and Zr0.06 was 56, 50, and 44 nm, respectively. The morphology of samples was assessed using TEM. Electrophysiological effects of ZrNFs in the cellular interaction process were revealed by the slower rate of electron transfer results in CV demonstration. Biocompatibility of synthesized ZrNFs was studied on A431 human epidermoid carcinoma epithelial cells. The cell viability was increased with an increasing the concentration of nanoflakes up to 6.50–100 μg/mL. The cell viability and observed IC50 values (44.25, 36.49, and 39.62 μg/mL) reveals that the synthesized ZrNFs using E. littorale extract is found to be efficient toxic to A431 cancer cell lines.