An integrated approach based on machine learning and data augmentation techniques has been developed in order to predict the stiffness modulus of the asphalt concrete layer of an airport runway, from data acquired with a heavy weight deflectometer (HWD). The predictive model relies on a shallow neural network (SNN) trained with the results of a backcalculation, by means of a data augmentation method and can produce estimations of the stiffness modulus even at runway points not yet sampled. The Bayesian regularization algorithm was used for training of the feedforward backpropagation SNN, and a k-fold cross-validation procedure was implemented for a fair performance evaluation. The testing phase result concerning the stiffness modulus prediction was characterized by a coefficient of correlation equal to 0.9864 demonstrating that the proposed neural approach is fully reliable for performance evaluation of airfield pavements or any other paved area. Such a performance prediction model can play a crucial role in airport pavement management systems (APMS), allowing the maintenance budget to be optimized.