Work coordinate setup is a time-consuming and difficult task in ultraprecision machining. The setup process determines the precision and tolerance of the machined parts. In ultraprecision machining, the table can be moved in the nanometer range, but the accuracy of the measuring device has not reached the nanometer accuracy range. Although several measurement methods have been proposed, the attained precision is still insufficient. Some methods also lose the precision when the sensor is changed with the tool after the work coordinate setup is completed. A work coordinate setup method proposed in this study could improve the precision and the measurement process using electron tunneling. Since the method can use the tool as a sensor probe, the changing process does not degrade the measurement precision. In addition, the proposed method can theoretically detect the distance between the tool and the workpiece in sub-nanometers like a scanning tunneling microscope. The simple system requires a precision current amplifier capable of measuring electron tunneling current in the picoampere to nanoampere range and a power supply. The method, installed on an ultra-precision machine tool, was tested on WC and aluminum material. The accuracy of the method was evaluated for applied voltage.