Among apex locators, the frequency dependent type is more accurate and convenient to use than others. However, the accuracy of the apex locator is still influenced by the presence of various electrolytes used in root canal treatments. In this study, we developed a frequency-dependent electronic apex locator minimizing the influence of electrolytes on the measurement of root canal lengths. It was confirmed that the two frequencies of 0.5 and 10 kHz are better than the conventional ones of 0.4 and 8 kHz. The impedance ratio of the two different frequencies represents the position of the file in root canal, and the voltage difference of the two frequencies represents the status of the fluid in the root canal. As a result of compensation using the voltage differences of the two frequencies, the errors decreased significantly on average from +0.54 mm to +0.18 mm in H2O2 solution (p < 0.01), and from -0.33 mm to -0.01 mm in NaOCl solution (p < 0.01) in the tooth model experiments.