In recent years, there is a growing interest in blending hydrogen with natural gas fuels to produce low-carbon electricity. It is important to evaluate the safety of gas turbine packages under these conditions, such as late-light off and flameout scenarios. However, the assessment of the safety risks by performing experiments in full-scale exhaust ducts is a very expensive and, potentially, risky endeavor. Computational simulations using a high fidelity CFD model provide a cost-effective way of assessing the safety risk. In this study, a computational model is implemented to perform three-dimensional, compressible, and unsteady simulations of reacting flows in a gas turbine exhaust duct. Computational results were validated against data obtained at the simulated conditions in a representative geometry. Due to the enormous size of the geometry, special attention was given to the discretization of the computational domain and the combustion model. Results show that CFD model predicts the main features of the pressure rise driven by the combustion process. The peak pressures obtained computationally and experimentally differed by 20%. This difference increased up to 45% by reducing the preheated inflow conditions. The effects of rig geometry and flow conditions on the accuracy of the CFD model are discussed.