Among several parameters affecting the fatigue life of the welded joints, the size effect and weld quality are the main focus of the current study. Fatigue design technical documents consider the thickness effect by reducing the S-N curve for joints thicker than the reference thickness value. Yet, limited attention has been paid to the thinness effect, where the specimens gain life due to decreasing thickness. Understanding the connection between weld profile geometry and fatigue strength is also imperative for assessing welded joints against repeated loads, as geometrical irregularities lead to local stress raising and decrease fatigue life. In this study, several fatigue test series were performed on non-load carrying welded joints with 2- and 16-mm thicknesses under uniaxial constant amplitude loading, resulting in S-N curves to analyse the influence of thickness on fatigue strength. For each test specimen, the variation of weld shape along the weld seam is measured using a laser scanning tool. Assessment of fatigue test results and weld profile measured data helps better understand the uncertainty and variation in fatigue life and the relationship between fatigue strength with specimen thickness and the weld quality. The results indicate that there is a beneficial effect from reducing thickness and increased weld quality.