In this paper, a posteriori error in finite element analysis for ship structure problems is considered. Error is estimated in element-wise fashion in order to decrease computing time and memory use. The major difficulties in the element-wise error estimation are satisfying the self-equilibrium condition and allocation of traction discontinuity along element boundaries. An optimal procedure is used for satisfying the self-equilibrium condition, while traction discontinuity along element boundaries is allocated based on the ratio of stiffness of adjacent elements for each degree of freedom. Several sample problems are solved for showing the capability of the proposed method. The accuracy of the method is ensured by comparing the estimated error and referenced error. A lower stool part of a bulk carrier and transverse ring of oil tanker are analyzed as an application of the method to the real problem. A posteriori error in the averaged stress distribution is also considered.