This paper presents a finite element analysis and its related experimental test of corrugated steel web beams subjected to fatigue loading. A particular focus in this study was set on the fatigue failure arising from the web-to-flange welded joint of the corrugated steel web beam. A detailed three-dimensional finite element model which explicitly includes the geometry of the web-to-flange welds along the corrugated web was developed to simulate the test corrugated web beam. The finite element model is verified by comparing with related fatigue experimental test results. The effective notch stress approach was also applied to analyse the web-to-flange welded joint replicating the local critical region in the corrugated web beam. The fatigue strength of the web-to-flange welded joint was evaluated and compared numerically by considering the stress distribution at potential fatigue crack initiation location. The fatigue life of the corrugated web beam was assessed numerically by incorporating material S-N relation and employing fracture mechanics approach. The comparison with the fatigue test results show that it is possible to expect the fatigue crack failure arising at the weld root or weld toe corresponding to the sections with reference angle using the effective notch stress analysis. The range of these predictions was evaluated by comparing with fatigue test results with accuracy and can be considered between AASHTO fatigue categories B and B’. The parametric notch stress analysis incorporating the influences of corrugation angle was performed and demonstrates it is possible to expect the fatigue crack failure arising at the weld root or weld toe. Finally, a practical solution for possible fatigue life enhancement of such structure is proposed by decreasing the corrugation angle or smoothing the intersection geometry of the corrugated web is suggested together with a moderate increase of the flange thickness.