Objective To establish a new method to measure the elastic modulus of living circulating tumor cells (CTCs) by micropipette aspiration. Methods Living CTCs were enriched by commercial microfluidic chips and identified individually using EpCAM antibody under fluorescence microscope. The elastic modulus of CTCs was measured using micropipette aspiration and compared with cancer cell lines. Results For the elastic modulus of different cancer cell lines, heterogeneity was found not only between the different types of cancer cell lines but also inside the same cell line. The CTCs in breast cancer had a smaller elasticity modulus compared with MCF-7 cancer cell line. Conclusions This method can measure the elastic modulus of living CTCs, which provides cell mechanics data for studying the relationship between physical properties of CTCs and diagnosis of cancers, as well as developing the physical biomarkers of tumor cells.