It is known that fatigue strength is affected by stress concentration depended on local shape of weld toe and welding residual stress. Fatigue strength of welded build-up structures decreases considerably because there are large tensile residual stresses and stress concentration at the fatigue crack initiation part in these structures. Authors showed that fatigue strength of the corner boxing joints and continuous fillet weld joints with load carrying girder increases very much by turning the tensile residual stress to compressive ones. Flame line heating on appropriate part enables to change the residual stress distribution. These results show that residual stress has a considerable influence on fatigue strength of welded build-up structures. Residual stress at the fatigue crack initiation part depends on welding procedure sequence near this part. Because the change of welding sequence means the change of thermal cycle given into this part by welding. The purpose of this paper makes clear the effect of welding procedure sequence on residual stress distribution and fatigue strength. Two different welding sequence specimens which have continuous fillet weld joints with load carrying girder were used. One of fatigue crack initiation part is the toe of final welding. The other is different part from final welding. Residual stress and fatigue life was investigated by using these specimens. Moreover, the estimation of residual stress distribution taking the welding sequence into consideration was carried out by using elastic finite element analysis based on inherent stress method. As a result of these investigations and analyses, it is clear that welding sequence has a considerable influence on residual stress distribution and that fatigue strength can be enhanced considerably by changing of welding sequence.