This paper proposes a new hybrid strategy to optimally design membrane separation problems. We formulate the problem as a Non-Linear Programming (NLP) model. A common approach to represent the physical behavior of the membrane is to discretize the system of differential equations that govern the separation process. Instead, we represent the input/output behavior of the single membrane by an artificial neural network (ANN) predictor. The ANN is trained on a dataset obtained through the MEMSIC simulator. The equation form of the trained predictor (shape and weights) is then inserted in the NLP model at the place of the discretized system of differential equations. To improve the ANN accuracy without an excessive computational burden, we propose data augmentation strategies to target the regions where densify the dataset. We compare a data augmentation strategy from the literature with a novel one that densifies the dataset around the stationary points visited by a global optimization algorithm. Our approach was validated using a relevant industrial case study: hydrogen purification. Validation by simulation is performed on the obtained solutions. The computational results show that a data augmentation smartly coupled with optimization can produce a robust and reliable design tool.