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It is well known that Boussinesq turbulent-viscosity hypothesis can introduce uncertainty in predictions for complex flow features such as separation, reattachment, and laminar-turbulent transition. This study adopts a recent physics-based uncertainty quantification (UQ) approach to address such model form uncertainty in Reynolds-averaged Naiver- Stokes (RANS) simulations. Thus far, almost all UQ studies have focused on quantifying the model form uncertainty in turbulent flow scenarios. The focus of the study is to advance our understanding of the performance of the UQ approach on two different transitional flow scenarios: a flat plate and a SD7003 airfoil, to close this gap. For the T3A (flat-plate flow) flow, most of the model form uncertainty is concentrated in the laminar-turbulent transition region. For the SD7003 airfoil flow, the eigenvalue perturbations reveal a decrease as well as an increase in the length of the separation bubble. As a consequence, the uncertainty bounds successfully encompass the reattachment point. Likewise, the region of reverse flow that appear in the separation bubble is either suppressed or bolstered by the eigenvalue perturbations. In this context, the UQ methodology is applied to transition and show great results. This is the first successful RANS UQ study for transitional flows.