This manuscript presents an experimental study to evaluate the applicability of the ultrasonic pulse-train Doppler method (UPTD) to the disturbed flow in a pipe. The UPTD can expand the detectable velocity range compared with the conventional ultrasonic pulse Doppler method and has an advantage of trouble-free installation into conventional hardware. Comparative experiments were conducted using two different transducer frequencies, 1 MHz and 4 MHz. The UPTD was only applied to the 4-MHz condition to expand the velocity range fourfold, which is equal to the velocity range of a 1-MHz transducer. The probability density distributions of the measured velocities were almost the same between 1 MHz and 4 MHz, even though the measurement position was not only downstream of a long straight pipe but also downstream 10 or 5 pipe diameters from an obstacle plate. To estimate the influence of aliasing on the velocity measurement for a large fluctuating flow, experiments using a 2-MHz transducer were also conducted. These results indicated that it is possible to estimate the standard deviation of the velocities measured under the aliasing condition, and the accuracy of flow rate measurement decreases when the standard deviation of the velocity exceeds the measurable velocity by approximately twice. Additionally, the flow rate by the 1-MHz transducer was about −2% smaller than that by the 4-MHz transducer for both the straight pipe and disturbed conditions. Through the validation of the influence of the measurement volume between 1 MHz and 4 MHz conditions, the flow rate difference was found to be likely due to the influences of not only the measurement volume but also the standing wave formed by the pulses reflected on the opposite pipe wall.