Today’s climate and energy challenges are driving the use of decarbonised and renewable alternative fuels in power generation and transportation. Hydrogen as a fuel is a good candidate to meet these requirements, as it offers no carbon emissions and can play the role of an energy carrier to store excess energy produced by renewable energy. Nonetheless, the production of NOx needs to be assessed. For this reason, this study proposes high-fidelity Large Eddy Simulations (LES) with detailed NOx analyzes of a partially premixed lean swirling H2-air flame. The chosen configuration is the technically premix hydrogen injector measured at the Berlin Institute of Technology (TUB) in Germany. A novel kinetic scheme for H2-air comprising 15 species and 47 reactions is developed to take into account all NOx pathways. To accurately solve the combustion process and the NOx production level, static mesh refinement (SMR) and conjugate heat transfer (CHT) are applied to the LES modeling and their impact on the numerical predictions is evaluated. A detailed analysis of the preferential diffusion and formation of NO is presented, demonstrating that the proposed numerical model, combined with the novel chemical kinetic scheme, is able to correctly predict complex transport phenomena observed in lean turbulent hydrogen flames and to predict their NO dynamic formation accounting for both primary and secondary (N2O and NNH) NOx pathways.