There is a plethora of methods in the global literature that can be used to measure CO2 emissions from electrified transport. But are these methods reliable, and do they offer us a true view of how much exactly of this greenhouse gas is being produced by electric rail transport? We answer this question by proposing an improved CO2 emission estimation model based on cargo transport. Unlike other works, our studies include four crucial steps: (1) estimation of energy consumption in electrified rail cargo transport; (2) estimation of energy losses in the railway traction system and high voltage transmission lines; (3) CO2 emission estimation in traditional powerhouses; and (4) determination of the intensity of the CO2 emissions from electrified rail cargo transport. Based on our method, we concluded that the intensity of CO2 depends not only on the type of fossil fuel used for energy production but also on the parameters of the cargo train, such as its length and weight or the total number of wagon axles (which depend on wagon type). The achieved intensity of CO2 emissions in electrified rail cargo transport slightly varies from those reported in the global literature. Among the most important reasons responsible for this are the conditions under which these tests were conducted. Nevertheless, our results shed new light on how CO2 should be measured. We proved that the decarbonization of electrified rail cargo transport will never be possible without infrastructure modernization. In addition, based on a case study, we also delivered knowledge on how to reduce the environmental impact of electrified rail cargo transport.