We propose a new technique for evaluating empirical site effects in time domain, extending the concept of Birgören and Irikura (2005). They developed a method for estimating coherent site effects by averaging wavelet coefficients of the Meyer-Yamada wavelet for many seismic records. In general, site effects consist of coherent and incoherent signals. If only coherent site effects are evaluated, it is underestimated compared with true site effects. We propose a new averaging approach to accurately evaluate both the coherent and incoherent signals.