In this paper, we propose a low-complexity and low-latency method of FFT based channel estimation for Mobile OFDM systems. Mobile WiMAX system and LTE are next generation communication systems which adopt OFDM systems to achieve high mobility and a high data rate. Especially for high mobility communication systems, efficient channel estimation, technology should be developed. The proposed channel estimation calculates threshold value of channel impulse response (CIR) using discrete wavelet transform (DWT) in a frequency domain. In the experimental results, the proposed method increased performance with low-complexity and low-latency. Implementaion and simulation results show that the proposed method reduced the latency about 43% compared with conventional DFT based channel estimators.