During the last two decades, lots of efforts have been devoted to resolve thermal stratification phenomenon and primary water environment issues. While several effective methods were proposed especially in related to thermally stratified flow analyses and corrosive material resistance experiments, however, lack of details on specific stress and fatigue evaluation make it difficult to quantify structural behaviors. In the present work, effects of the thermal stratification and primary water are numerically examined from a structural integrity point of view. First, a representative austenitic nuclear piping is selected and its stress components at critical locations are calculated in use of four stratified temperature inputs and eight transient conditions. Subsequently, both metal and environmental fatigue usage factors of the piping are determined by manipulating the stress components in accordance with NUREG/CR-5704 as well as ASME B&PV Codes. Key findings from the fatigue evaluation with applicability of pipe and three-dimensional solid finite elements are fully discussed and a recommendation for realistic evaluation is suggested.