The separation time-overlapping ultrasound signals is necessary to obtain accurate estimate of transit time and material properties. In this letter, a method to determine the optimal transform order of fractional Fourier transform (FRFT) for decomposition of overlapping ultrasonic signals is proposed. The optimal transform order is obtained by minimizing the mean square error (MSE) between the output and the reference signal. Furthermore, windowing in FRFT domain is discussed. Numerical simulation results show the performances of the proposed method in separating signals overlapping in time.