Emission data, together with meteorology, is the most important input to air quality models. In this work we compare two simulations, performed with the fine resolution atmospheric multi-pollutant exchange (FRAME) model. In the first model run, we use an emission inventory prepared for Poland by downscaling the national total emissions to a 5 km × 5 km resolution grid. For the second model run, we replace the NOx road transport emission with the TNO-MACC II emission inventory available for the entire Europe. The grid mesh of both emission inventories was unified for this work to a 5 km × 5 km resolution, as required by the FRAME model. The FRAME model is run for the year 2008 and compared with the NOx measurements. Both inventories are in close spatial agreement, with a grid to grid correlation coefficient of 0.75. The FRAME model run with TNO-MACC II emission inventory shows better agreement with NOx measurements gathered at 106 stations if the mean bias is considered. For the model run with TNO-MACC II inventory, bias is −0.7 μg m³, and the RMSE is 8.19 μg m³. The bias for the FRAME model run with the national road transport emission inventory is −3.10 μg m³ and the RMSE 7.97 μg m³.