Computerized analysis of Doppler ultrasound signals can aid early detection of asymptomatic circulating emboli. For analysis, physicians use informative features extracted from Doppler ultrasound signals. Time -frequency analysis methods are useful tools to exploit the transient like signals such as Embolic signals. Detection of discriminative features would be the first step toward automated analysis of embolic Doppler ultrasound signals. The most problematic part of setting up emboli detection system is to differentiate embolic signals from confusing similar wave-like patterns such as Doppler speckle and artifacts caused by tissue movement, probe tapping, speaking etc. In this study, discrete version of fractional Fourier transform is presented as a solution in the detection of emboli in digitized Doppler ultrasound signals. An accurate set of parameters are extracted using short time Fourier transform and fractional Fourier transform and the results are compared to reveal detection quality. Experimental results prove the efficiency of fractional Fourier transform in which discriminative features becomes more evident.