The current approaches for the characterization of cellular electrical properties normally require a tested sample with high cell quantity, restricting their application in the cases in which the cell number in a sample is limited. To address this issue, this study presented a low-sample-loss microfluidic system capable of characterizing the size-independent electrical properties (e.g., specific membrane capacitance and cytoplasm conductivity) of single cells. In the design, a capillary tube was used to transfer cells directly into the entrance of a microfluidic constriction microchannel to possibly minimize cell sample loss. Results revealed that the microfluidic system was able to significantly reduce the sample loss phenomenon, by which the cell processing ratio could be raised from the original 0.2% to 49.3–60.0%. As a demonstration, moreover, the feasibility of using the proposed method for the identification of the EpCAM-positive CTCs after a CTC isolation process, and for the differentiation of the EpCAM-positive CTCs of three different (hepatic, oral and lung) cancer types were experimentally evaluated. Within the experimental conditions explored, our findings indicated that the proposed method was able to significantly identify the EpCAM-positive CTCs from the surrounding EpCAM-negative cells, as well as to differentiate the EpCAM-positive CTCs of the three different cancer types tested, based on their unique electrical properties of cells. As a whole, the proposed microfluidic system was found useful for the identification of CTCs after a conventional CTC isolation process. In addition to CTC identification, the proposed method might hold potential for the detection of a specific cell species in a cell suspension sample with limited cell quantity.