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The applicability of system-in-package (SiP) type structures may be limited due to chip-to-chip thermal interactions. Therefore all significant heat sources have to be considered in the design to ensure safe operating temperatures. In this paper, we propose a generic compact thermal model (CTM) synthesis method for multichip packages that takes dynamic chip-to-chip interactions and different boundary conditions into account. The method is demonstrated with a stacked three-dimensional multichip module. Dynamic thermal characteristics of the module are studied by means of detailed finite element simulations and the results are considered as reference data in the synthesis. The CTM is optimized to diverse conditions typical to the application-specific environment, and the accuracy of the model is found sufficient for thermal design purposes.