This paper describes an evaluation method of primary stress in three dimensional (3-D) structures. In “Design by Analysis” for nuclear components, the stresses in structures are classified into the primary and the secondary stresses. The primary stress in axisymmetric structures can be evaluated by linealization of stress distribution in the specified section, but it is difficult to define the evaluation section in the 3-D structures, and to evaluate the primary stress with the conventional procedure. From this reason, the alternative evaluation method is needed. In this study, the evaluation method of primary stress in 3-D structures with elastic-plastic analysis is proposed utilizing the feature of primary stress that is independent from stress redistribution. The proposed method is verified through application to example problems.