Hot-spot stress concept is commonly used for fatigue strength assessment. Hot-spot stress is generally defined as the structural concentration stress at the toe of welding bead excluding the concentration stress induced by the welding bead itself. This stress component cannot be obtained directly, so that some estimation methods have been proposed. However, existing methods are the extrapolation method based on some assumption of stress distribution considered not to be based on the theoretical background. This paper presents a new estimation method of the hot-spot stress based on a theoretical back-ground for flat steel plate structures with a pad plate. Firstly, the solid element FE analysis with fillet welded modeling is carried out and the separation method of the structural concentration stress from the total stress is proposed, namely hot-spot stress can be obtained logically. This procedure indicates that a hot-spot stress can be obtained directly by shell element FE analyses. Therefore, modeling technique of the flat steel plate structure with pad plate by the shell element FE model is established and FE analyses by the shell model are carried out, secondary. Finally, hot spot stresses obtained by the new method and existing methods are compared and evaluated. And it is found that the existing method gives lower value of hot-spot stress and proposed new method is considered to be a rational method.