The scheme and procedure for thermal fatigue estimation of a thermally stratified branch line were developed. One-way FSI (fluid and structure interaction) scheme was applied to evaluate the thermal stratification piping. Thermal flow analysis, stress analysis and fatigue estimation were performed in serial order. Finally, detailed monitoring locations and mitigation scheme for the integrity maintenance of piping were recommended. Ali wall mesh and transient temperature distribution data obtained from the CFD (computational fluid dynamics) analysis were directly imported into the input data of stress analysis model without any calculation for heat transfer coefficients. Cumulated usage factors for fatigue effect review with nodes were calculated. A modified method that combines ASME Section III, NB-3600 with NB-3200 was used because the previous method cannot consider the thermal stratification stress intensity. As the results of evaluation, the SCS (shutdown cooling system) line, branch piping of the RCS (reactor coolant system) line, shows that the CUF (cumulative usage factor) value exceeds 1.0, ASME Code limit, in case thermal stratification load is included. The HPSI (high pressure safety injection) line, re-branch piping, shows that temperature difference between top and bottom of piping exceeds the criterion temperature, $28^{circ}C$, and that the CUF value exceeds 1.0. Therefore, these branch pipings require a detailed review, monitoring or analysis. In particular, it is recommended that the HPSI piping should be shifted backward to decrease the influence of turbulent penetration intensity from the RCS piping.