When operating under lean fuel–air conditions, flame flashback is an operational safety issue in stationary gas turbines. In particular, with the increased use of hydrogen, the propagation of the flame through the boundary layers into the mixing section becomes feasible. Typically, these mixing regions are not designed to hold a high-temperature flame and can lead to catastrophic failure of the gas turbine. Flame flashback along the boundary layers is a competition between chemical reactions in a turbulent flow, where fuel and air are incompletely mixed, and heat loss to the wall that promotes flame quenching. The focus of this work is to develop a comprehensive simulation approach to model boundary layer flashback, accounting for fuel–air stratification and wall heat loss. A large eddy simulation (LES) based framework is used, along with a tabulation-based combustion model. Different approaches to tabulation and the effect of wall heat loss are studied. An experimental flashback configuration is used to understand the predictive accuracy of the models. It is shown that diffusion-flame-based tabulation methods are better suited due to the flashback occurring in relatively low-strain and lean fuel–air mixtures. Further, the flashback is promoted by the formation of features such as flame tongues, which induce negative velocity separated boundary layer flow that promotes upstream flame motion. The wall heat loss alters the strength of these separated flows, which in turn affects the flashback propensity. Comparisons with experimental data for both non-reacting cases that quantify fuel–air mixing and reacting flashback cases are used to demonstrate predictive accuracy.