In AGPS method, user position can be obtained even in the shadow region by improving signal sensitivity. A hybrid long integration scheme employing both coherent and non-coherent integration method is commonly used in AGPS receivers. Because coherent loss increases as residual frequency become large, residual frequency should be minimized to maximize coherent integration gain. This paper presents performance analysis of residual frequency estimator using FFT in fine-time assistance AGPS method. Considering the hardware complexity and the estimation accuracy, optimal length of FFT is proposed for GPS L1 C/A signal. Signal sensitivity for estimating the residual frequency is also analysed. By field experimental results, it is found that the residual frequency can be successfully estimated using 1 second snap-shot data when GPS signal strength is larger than -150 dBm and its RMS error is 3Hz.