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Nowadays, major trends in the design of electronic products are toward multifunction and miniaturization. To meet these trends, system-in-package (SiP) has been adapted as one of the core packaging technologies for many product applications. Among the various types of SiPs, SiP with embedded dies has become important due to the smaller size achieved through embedded dies and better electrical performance by the shorter interconnection length. However, reliability data of the SiP with embedded dies have not been reported yet. Therefore, it is necessary to investigate the reliability of the SiPs with embedded dies and the effect of the embedded die on the SiP reliability. Of the several reliability tests, a detailed thermal cycling test (T/C test) was performed on board-level packaged samples. A finite element method (FEM) simulation was also performed to find out the stress and strain distribution of ball grid array (BGA) solder positions and to predict the potential failure sites under the T/C test. Through this paper, it was found that the failure position of the BGA changed from the corner solder ball position of the conventional BGA package, where the largest distance from neutral point was, to the inner BGA solder ball positions, where the edge of embedded die was located, due to the complicated structure of embedded die SiPs. Furthermore, FEM results showed that the inner site of the BGA is more vulnerable than the corner BGAs. This was well matched with experimental results.