A multilayer perceptron neural networks (MLPNN) model is developed for robust and quick prediction of stacking fault energy (SFE) to overcome the challenges faced in the calculation of SFE via experimentation and atomistic calculations in FCC medium entropy alloys (MEA). The present investigation employs a three-step hybrid feature selection approach to obtain a comprehensive understanding of the prominent features that influence the SFE, as well as the interrelationships among these features. The feature space encompasses various features related to composition, lattice stability, and elemental properties, of medium entropy alloys (MEAs). The findings indicate that the estimation of SFE relies on five crucial factors: temperature, lattice stability, specific heat, ionization energy, and Allen electronegativities. Furthermore, a mathematical relationship for the estimation of the SFE is derived, considering the various influencing and prominent factors. Consequently, the MLPNN model for robust SFE prediction in MEAs is developed and the performance is evaluated using R2 scores, with values of 0.87 and 0.85 obtained for the training and testing datasets, respectively. This efficient strategy introduces a novel opportunity for the engineering of SFE in the extensive range of alloy chemistry of MEAs, enabling the quick prediction of SFE, and facilitating the systematic exploration of new alloys for the development of mechanisms that may accommodate deformation through octahedral/partial slip, twinning, and/or transformation.