An engine air system for charge flow temperature estimation includes a charge air cooler outlet temperature sensor configured to provide a first temperature signal, an exhaust gas recirculation outlet temperature sensor configured to provide a second temperature signal, and a control module configured to receive the first temperature signal and the second temperature signal. The control module includes a charge flow temperature estimation module configured to determine an the estimated charge flow temperature at an intake manifold temperature sensing position based on a combination of the first temperature signal multiplied by an estimated fresh air fraction and the second temperature signal multiplied by an exhaust gas recirculation fraction.