In this study, the reduction factor of the code-defined site coefficient due to the embedment of a foundation was estimated for the seismic analysis of a building built on a soft soil site. This was done by utilizing the in-house finite element software P3DASS, which has the capability of pseudo 3D seismic analysis with nonlinear soil layers. A 30m thick soft soil site laid on the rock was assumed to be homogeneous, elastic, viscous and isotropic, and equivalent circular rigid foundations with radii of 10-70m were considered to be embedded at 0, 10, 20 and 30m in the soil layer. Seismic analyses were performed with 7 bedrock earthquake records deconvoluted from the outcrop records of which the effective ground acceleration was scaled to 0.1g. The study results showed that the site coefficients are gradually reduced except in the case of a small foundation embedded deeply in the weak soil layer, and it was estimated that the deviation of the site coefficients due to the foundation size was not significant. The standard reduction factor due to the foundation embedment were calculated adding the standard deviation to the average of 5 reduction factors calculated for 5 different foundation radii. Standard reduction factors for the site amplification factor were proposed for the practical amplification and the codes of KBC, etc., in accordance with the average shear wave velocity of the site, and the site class.