Start of fuel injection and fuel type are two important factors affecting engine performance and exhaust emissions in internal combustion engines. In the present study, a one-dimensional computational fluid dynamics solution with GT-Power software is used to simulate a six-cylinder diesel engine to study the performance and exhaust emissions with different injection timing and alternative fuels. Starting the fuel injection was from 10 °CA BTDC to the TDC with an interval between two units and from alternative fuel bases (diesel), including methanol, ethanol, diesel, and ethanol compounds, biodiesel and decane was used. To validate the model, a comparison is made between simulation data and experimental data (including torque and power) showing the validation error is less than 6.12% and indicating the software model validation. Also, the modeling results show that decane fuel has higher brake power and brake torque of more than 6.10 % while fuel is injected at 10 °CA BTDC compared to the base fuel, and illustrates a reduction of 5.75 % in specific fuel consumption due to producing higher power. In addition, with the advance of injection timing compared to baseline, the amount of CO and HC in biodiesel fuel reduces to 83.88% and 64.87%, respectively, and the lowest NOX emission with the retardation of starting injection, to decane fuel is awarded. In general, the results show that decane fuel could be a good alternative to diesel fuel in diesel engines when it starts fuel injection at 10 °CA BTDC.