In this research, the effect of alternative fuels and the inlet charged air temperature is numerically investigated on the performance of a turbocharged spark-ignition engine. For this purpose, a one-dimensional engine and turbocharger model is created in an engine simulation and performance analysis software and validated with former experimental results. Then, the model is run with four fuel types, including two gasoline types with different octane numbers and two ethanol–gasoline blend fuels—E25 and E85. In each case, the inlet charged air temperature is changed from cold to hot condition and performance characteristics such as the spark advance timing, brake torque, brake-specific fuel consumption and thermal efficiency, emissions and the ignition delay and combustion duration are obtained from simulation results. The results illustrate that by decreasing the inlet charged air temperature, the spark timing is more advanced due to less knock and the brake torque increases. Also, the brake-specific fuel consumption and the brake NOx and CO2 decrease and thermal efficiency increases in all fuel types. The results also demonstrate that in higher ethanol percent in blend fuels, all engine performance characteristics improve except brake-specific fuel consumption; as changing the fuel at constant fuel-to-air equivalence ratio from E25 to E85 in various revolutions per minute causes a 5.8% increase in the brake torque, 1.06% increase in the thermal efficiency, 43% and 3.9% decrease in the brake NOx and CO2 and 5.8 °CA decrease in the combustion duration, on average; while the brake-specific fuel consumption and the peak pressure increase 29% and 20%, respectively.