The present-day world is characterized by the intense development of air transport. However, along with it, significant problems appear. Among these problems, the most important are those relating to safety and negative impact of air transport on the environment. Air transport efficiency and profitability issues, although not critical, must also be taken into account because they decide about the intensity of development of this branch of transport. There are currently two large programs in Europe oriented at improving safety, environmental, and efficiency indicators. These are SESAR 2020 and Clean Sky 2, being a continuation of previous ones. One of the ways to reduce negative impact of air transport on the environment and improve its efficiency is to reduce fuel consumption and pollutants emissions resulting from fuel combustion. To find solutions with the abovementioned features, it is necessary to have sufficiently accurate models to estimate the amount of fuel consumed and the amount of pollutants emitted. Developing a sufficiently accurate model to determine fuel consumption and pollutants emission was performed. Due to the specificity of the missions carried out by passenger aircraft, the focus was on the cruise stage when aircraft flies at a constant altitude with a constant air speed. The result of the analysis was the development of methodology for fuel consumption and emission of main pollutants in cruise conditions. Specific fuel consumption is calculated for the thrust required for horizontal flight at cruising altitude. Emission indexes for CO, NOx, HC, and CO2 for the cruise have been determined based on known indexes for the landing and take-off cycle phase, after applying appropriate corrections. An illustration of the application of the developed methodology was the optimization of a medium-sized transport aircraft trajectory on a selected connection to determine a trajectory characterized by a minimum emission value taking into account weather conditions.