The present study aims to investigate differences in impedance between normal (SV-HUC-1) and cancerous (TCCSUP) human urothelial cell lines at multiple frequencies by using a micro-electrical impedance spectroscopy (µEIS) device. A µEIS device was designed to measure the impedance of SV-HUC-1 and TCCSUP cells as the cells passed the sensing electrodes in the microfluidic channel. The cellular impedance was measured at frequencies of 10, 50, 100, 500 kHz, and 1 MHz, and the impedance values were compared at each frequency to investigate differences between the two cell lines. Additionally, the linear correlation between impedance and frequency was analyzed. The number of SV-HUC-1 and TCCSUP cells measured was 13 and 9, 21 and 10, 16 and 24, 8 and 8, and 11 and 22 cells at the frequencies of 10, 50, 100, 500 kHz, and 1 MHz, respectively. TCCSUP had significantly smaller amplitudes than SV-HUC-1 at 10, 50, and 100 kHz (p = 0.030, p = 0.031, and p < 0.001, respectively). Moreover, significant differences in phase angle were observed between cell lines at 100, 500 kHz, and 1 MHz (p < 0.001 in all). A significant difference between cell lines in terms of amplitude and phase angle was observed concurrently at 100 kHz. The amplitude of both the cell lines was negatively correlated to frequency, while the phase angle presented no correlation. In conclusion, the µEIS device could effectively differentiate between SV-HUC-1 and TCCSUP on the basis of their impedance.