Warpage of semiconductor packaging substrate during or after manufacturing processes has been a serious issue in the electronics industry. We found that the packaging substrate, which has initial warpage at room temperature, changes its warpage orientation by flipping from a concave to a convex cylindrical shape during the thermal processing. In this paper, we demonstrate that the rotation of warpage orientation is attributed to viscoelastic properties of fiber reinforced polymer (FRP) packaging substrate by using finite element method (FEM) simulations and experiments. Due to the viscoelastic properties in FRP substrate, the specimen shape was converted into a saddle shape during the warpage directional transition and changed its orientation. In conclusion, it is shown that the viscoelastic property of FRP substrate is a critical factor in analyzing warpage orientation change and its behavior.