Welded structures under random loadings are usually susceptible to fatigue-induced failures that lead to significant economic and safety effects. However, accurately predicting these structures’ fatigue damage and life in the frequency domain remains challenging due to the limitations associated with using traditional weld stress extrapolation methods, such as nominal, hotspot, and notch stress methods. These methods struggle with precisely defining and characterizing the stresses at the weld toe and root as they vary depending on factors like weld stress concentration effects, joint geometry, and loading modes. This research introduces an Equilibrium Equivalent Structural Stress (EESS)-based frequency-domain fatigue analysis approach for welded structures subjected to random loading. The proposed method utilizes the EESS formulations, which are based on the decomposition and characterization of weld toe stresses with a single stress parameter, together with incorporating structural dynamic properties’ effects on the stresses acting on the weld joints and the corresponding accumulated fatigue damage of the structure. The numerical demonstration and validation of the proposed method have been performed using a welded Rectangular Hollow Section (RHS) T-joint structure subjected to stationary random fatigue loading. The proposed method’s fatigue damage and life results are compared with the fatigue test data and the equivalent hotspot stress extrapolation-based technique results.