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The general policy of the European Union in reducing greenhouse gas emissions is such that the increased average global temperature is kept below 2 °C. Many countries are looking for more effective solutions and methods to reduce carbon emissions. There are effective factors in the scheduling passenger and freight trains in the inter-city rail transport industry such as number of trains requested at the station, the number of stops, delays and waiting times for trains at the station which lead to increased fossil fuel consumption and carbon emission. In this paper, we want to present a new mixed integer non-linear model that can choose the best schedule for movement of passenger and freight shuttle trains on a single-line route of the railway network with the least environmental pollution. In this model, the carbon emission factor is based on the weight and prioritization of passenger and freight trains. Also, the average number of demands for using trains at a station and the number of planned or non-planned stops and delays at the middle stations are considered. Also, the proposed model selects the best plan for moving trains with the lowest carbon emissions caused by fuel consumption. To validate the proposed model, a case study of a crowded passenger and freight route of an inter-city railway network in Iran will be solved. We solve the real studied problem using the GAMS v24.9.1 optimization software with BARON solver. Finally, after sensitivity analysis of the results, we demonstrate the convenient and efficient performance of the same model in solving the raised problems in an applied manner. Image 10162 • A new model for reducing Carbon emissions through optimal scheduling of trains is developed. • We apply the carbon emission factor based on the weight and prioritization of passenger and freight trains. • We consider the number of planned and non-planned stops, delays, and waiting times of trains. • A real case study is applied for validating the proposed model. [ABSTRACT FROM AUTHOR]