Time delay estimation (TDE) is one of the critical technology in radar and sonar system. This paper proposed a new algorithm for TDE based on zero crossing (ZC). The basic model of zero crossing TDE is discussed, and the mean squared error with additive white Gaussian noise is derived by a theoretic equation. It is shown that the accuracy of TDE is a function of signal-to-noise ratio (SNR), signal frequency and numbers of ZC points. The ZC algorithm approaches a comparable accuracy with FFT method for high SNR, though with low computational complexity and low processing latency. The proposed zero crossing estimator is suitable for real-time applications.