In evaluation of the fatigue strength of large structural systems, the fatigue analysis via the finite element (FE) method is more useful than its experimental approach. However, in the fatigue analysis for the FE model containing millions of degrees of freedom (DOFs), to derive the local stress history by using entire FE model is considerably inefficient. Also, it is difficult to reflect the design changes repeatedly which are requested according to the calculated fatigue life. In this study, to resolve the inefficiency mentioned above, we present an efficient procedure for the fatigue analysis by employing the automated static condensation (ASC) method. In the proposed procedure, the critical local FE model requiring the fatigue assessment is designated as the target part to be remained, and the other parts are all omitted without the numerical errors through the ASC algorithm. After then, a new critical local FE model updating the stiffness effect of the omitted part is obtained, using this reduced model, we perform the fatigue analysis for the several structures, and show the several advantages than the traditional fatigue analysis procedure.