The proteolytic activity of cathepsin B in complex breast cell lysates have been measured with alternating current voltammetry (ACV) using ferrocene (Fc)-labeled-tetrapeptides immobilized on nanoelectrode arrays (NEAs) fabricated with vertically aligned carbon nanofibers (VACNFs). Four types of breast cells have been tested, including normal breast cells (HMEC), transformed breast cells (MCF-10A), breast cancer cells (T47D), and metastatic breast cancer cells (MDA-MB-231). The detected protease activity was found increased in cancer cells, with the MDA-MB-231 metastatic cancer cell lysate showing the highest cathepsin B activity. The equivalent cathepsin B concentration in MDA-MB-231 cancer cell lysate was quantitatively determined by spiking recombinant cathepsin B into the immunoprecipitated MDA-MB-231 lysate and the HMEC whole cell lysate. The results illustrated the potential of this technique as a portable multiplex electronic device for cancer diagnosis and treatment monitoring through rapid profiling the activity of specific cancer-relevant proteases.