This paper describes a numerical method for pile foundation subjected to earthquake loading using dynamic Winkler foundation model. To verify the numerical method, shaking table tests were carried out. In shaking table tests, accelerations and pile bending moments were measured for single pile and pile groups with a spacing-to-diameter ratio of 2.5 under fixed input base acceleration. In numerical analysis, the input base and free field accelerations measured from shaking table tests were used as input base motions. Based on the results obtained, free field acceleration was magnified relative to input base acceleration, whereas pile head accelerations reduced relatively to free field acceleration for soil-pile interaction. Measured and predicted bending moments for both cases have maximum value within the distance 10cm(4d) from the pile top. However, there are some differences between the results of numerical analysis and shake table test below 10cm(4d) from the pile top.