Utilization of thin plates together with laser-based welding processes allows manufacturing of large weight efficient steel structures. However, the fatigue strength of welds in thin-plate structures with plate thicknesses below 5 mm is observed to have large variation, which brings challenges to fatigue strength assessment. One possible reason for this variation is the increased influence of actual weld geometry that is neglected in common fatigue strength assessment approaches utilizing geometry idealization. To reveal this influence the fatigue strength of 3 mm thick laser-hybrid welded butt joints were studied using the measured microscale weld geometry and the notch stress approach. Notch stresses were defined using Neuber's stress averaging approach which allows the determination of the fatigue-effective stress without fictitious geometric modifications. For the studied specimens the large scatter of fatigue strength in the high-cycle region could be explained using this approach with high-resolution weld profile measurements combined with thorough finite-element analysis. It was observed that axial misalignment in narrow laser-hybrid welds causes a significant notch stress increase on the root side reducing the fatigue strength dramatically in terms of structural and nominal stress. In order to capture the increased notch stress it is crucial to use a significantly smaller stress averaging length than commonly assumed for welded joints.