Thermal stratification has continuously caused several piping failures in nuclear power plants since the early 1980s. However, this critical thermal effect was not considered when the old nuclear power plants were designed. Therefore, it is urgent to evaluate this unexpected thermal effect on the structural integrity of piping systems. In this paper, the thermal effects of stratified flow in two different safety injection piping systems were investigated by using a coupled CFD-FE method. Since stratified flow is generally generated by turbulent penetration and/or valve leakage, thermal stress analyses as well as CFD analyses were carried out considering these two primary causes. Numerical results show that the most critical factor governing thermal stratification is valve leakage and that temperature distribution significantly changes according to the leakage path. In particular, in-leakage has a high possibility of causing considerable structural problems in RCS piping.