This paper researches on the implementation of an ultrasonic time-of-flight (TOF) measuring system by the difference of the peak time sequences (PTSs) of dual frequencies. The process to develop appropriate implementation parameters was demonstrated. Critical characteristics of the transient behavior of the PTS were studied, and their counteracting data processing measures were devised in the process. Obtaining the PTS by averaging repeated test data and the linear regression on the PTS was found to be effective in uncovering the actual TOF of the first wavefront with high precision. A PC-based test bench was built to test the characteristics and to verify the performance of the new TOF measurement system. In our TOF measurement over the distance of 145 cm, a standard deviation (STD) of 0.0113 of a period was achieved by a nominal driving wave period of 25.6 μs (39 kHz) and a frequency difference factor of 0.0048. When applied to a distance measurement, the worst STD of 0.097 mm was achieved with a relative distance ranging up to 1450 mm, given the nominal driving wavelength of 8.6 mm. This new dual-frequency PTS-based TOF measurement system can be economically embedded in a microcontroller, together with a field-programmable gate array, and some simple transistors that are suitable for positioning mobile units indoors or in small open-field environments.