From the manufacturing viewpoint, overlapping thin sheets can provide a substantial geometrical improvement in welded hollow sections compared to butt-welded cross-sectional details. However, the plate eccentricity and non-penetrating fillet welds make the joints susceptible to fatigue failures under transversal cyclic loads. This work experimentally investigates the fatigue strength of overlap joints prepared with gas metal arc welding in the single-sided fillet weld configuration. Fatigue tests were carried out on the lap joints made of S960 ultra-high-strength steel (UHSS) grade under uniaxial constant amplitude axial loading employing both pulsating tension (applied stress ratio of R ≈ 0) and pulsating compression (R ≈ -∞). In addition, the lap joints were prepared with both straight welds (the welds transverse to the loading direction) and inclined welds (the welds with a 30° inclement angle from the transversal direction) to investigate the shear stress effects on the joints’ fatigue performance. Plasma butt-welded samples were tested as a reference join type. For the plasma butt-welded joints, the recommended detail category of FAT71 in the nominal stress system for weld root failures in single-sided butt welds was observed clearly conservative—a mean fatigue strength of Δσc,50% = 130 MPa with a fixed slope parameter of m = 3 was obtained. Compared to the butt-welded joints, a significant decrease in fatigue strength capacity was found in the lap joint specimens with misalignment factors of km > 3.0. The failure locations were also different in joints subjected to the tension and compression loads. The shear load did not majorly contribute to the changes in the fatigue strength capacity compared to the joints subjected to the transversal normal stress.