Ultrasonic measuring systems have high speed response, good accuracy and they are used in measuring fluid velocity and distance. Techniques based on time difference and signal processing have been used to time of flight estimation in order to reduce uncertainties. This work presents the development of a new methodology for time of flight estimation with ultrasound signals for wind speed measurement. The proposed method, based on the extended Kalman filter, uses a model for indirect time of flight measurement, through signal amplitude measurements of the receiving transducer. Experimental results performed using a wind tunnel, showed a performance of the proposed technique with time of flight values with an accuracy comparable to the phase difference technique in frequency domain, however without restricting the measurement range to one signal cycle (2π).