Thermal-induced distortion prediction of thin shell structures is a challenging task. It often involves highly nonlinear buckling behaviour, where the critical buckling temperature and post-buckling deformations are very sensitive not only to structural stiffness and boundary conditions but also minute geometric imperfections (a.k.a., “surface quality”) of the incoming parts. In the present work, novel Computer Aided Engineering (CAE) methods were developed to predict the thermal-induced distortion of automotive Body-in-White (BIW) panels during paint shop oven-baking processes. The CAE methodology consist of a set of three Finite Element Analysis (FEA) procedures, i.e., thermal-buckling mode analysis, thermo-structural analysis, and imperfection analysis. Two vehicle level case studies showed that simulations successfully predicted the thermal-induced distortion for panels such as the Body Side Outer (BSO) header. It was concluded that the distortion depends primarily on the temperature difference between the BSO and the rest of the BIW during the oven-baking process, rather than the temperatures themselves. Body panel forming quality (e.g., residual stresses and thickness thinning) and assembly dimensional quality were also found to impact the distortions.