An accurate air flow rate model is critical for high-quality air-fuel ratio control in Spark-Ignition engines using a Three-Way-Catalyst. Emerging Variable Valve Timing technology complicates cylinder air charge estimation by increasing the number of independent variables. In our previous study (SAE 2004-01-3054), an Artificial Neural Network (ANN) has been used successfully to represent the air flow rate as a function of four independent variables: intake camshaft position, exhaust camshaft position, engine speed and intake manifold pressure. However, in more general terms the air flow rate also depends on ambient temperature and pressure, the latter being largely a function of altitude. With arbitrary cam phasing combinations, the ambient pressure effects in particular can be very complex. In this study, we propose using a separate neural network to compensate the effects of altitude on the air flow rate. A predictive, high-fidelity simulation tool is used to generate training samples for the altitude compensation ANN. Compared with a test-based approach both developmental cost and time are reduced. The effectiveness of the proposed approach is evaluated and validated by both engine dynamometer tests and in-vehicle tests.