Rotary engines offer a highly attractive solution for uncrewed aerial vehicles (UAVs) and portable power generation, thanks to their compact design, high power-to-weight ratio, fewer moving parts, and ability to operate on multiple fuels. Despite their promising advantages, these engines still require significant improvements to match the efficiency and lifespan of traditional reciprocating internal combustion engines. In particular, fuel consumption is impacted by heat losses due to the high surface-to-volume ratio of the combustion chamber, as well as the unfavorable interaction between the rotor and stator, which slows down flame propagation. To address these challenges, computational fluid dynamics (CFD) has become an important tool for the study and optimization of Wankel engines, providing insight into how fuel efficiency is influenced by the complex interactions between combustion chamber design, flame dynamics, flow characteristics, and turbulence distribution. This work presents a CFD methodology for simulating gas exchange and combustion in Wankel engines. The proposed approach considers the contemporary operation of the three working chambers whose mesh is deformed and dynamically connected with the intake and exhaust ports. A flamelet model predicts the premixed combustion process. The proposed methodology has been validated under operating conditions representative of UAV applications, involving constant-speed operation with variable loads to mimic different altitudes. Results from CFD simulations were compared against experimental data, including in-cylinder pressure and heat release rate, as well as 1D engine simulation data to analyze the gas exchange processes. The findings demonstrate that this CFD-based approach can be applied to design and optimization of Wankel engines, offering high accuracy at a reduced computational cost.