A system and method for controlling an engine involves providing a pumping torque estimation model. The model distinguishes between pumping losses due to throttling and pumping losses due to valve flow losses. The model is implemented by a pair of look-up tables. The data in each look-up table reflect Pumping Mean Effective Pressure (PMEP), which is indicative of the pumping work. The throttling loss table provides a first contribution based on an engine delta pressure. The valve flow loss table provides a second contribution based on an engine speed and a relative airload. The first and second contributions are summed and then multiplied by a predetermined factor to convert the pumping work (PMEP) into pumping torque. The model will work with naturally-aspirated, turbo-charged and super-charged air induction configurations and provides improved altitude compensation. The model will also work with both spark-ignition and compression-ignition configurations.