Drone dynamics are affected by flight condition uncertainties, such as the surrounding structure, gust disturbance, and rotor damage, resulting in the deterioration of flight performance and safety. Real-time modeling of drone dynamics plays an important role in flight safety. In this study, the on-board measurement of downwash speed, which is an important parameter in drone dynamics, was performed using ultrasonic passing-time information. In this method, ultrasonic transmitters and receivers were arranged below the rotor, and the passing time in the downwash was estimated using an extended Kalman filter, which was designed for the constructed ultrasonic propagation dynamics model. It was validated that the proposed method is sufficiently robust to accurately estimate the downwash speed in a disturbed flow under a rotating rotor.