There is an increasing demand within consumer-neuroscience (or neuromarketing) for objective neural measures to quantify consumers’ preferences and predict responses to marketing campaigns. However, the properties of EEG raise difficulties for preference prediction: small datasets, high dimensionality, elaborate manual feature extraction, intrinsic noise, and between-subject variations. We aimed to overcome these limitations by combining unique techniques within a Deep Learning (DL) framework, while providing interpretable results for neuroscientific and decision-making insight. In this study, we developed a DL model to predict subject-specific preferences based on their EEG data. In each trial, 213 subjects observed a product’s image, from 72 possible products, and then reported how much they were willing to pay (WTP) for the product. The DL employed EEG recordings from product observation to predict the corresponding reported WTP values. Our results showed 75.09% test accuracy in predicting high vs. low WTP, surpassing other models and a manual feature extraction approach. Meanwhile, network visualizations provided the predictive frequencies of neural activity, their scalp distributions, and critical timepoints, shedding light on the neural mechanisms involved with evaluation. In conclusion, we show that DLNs may be the superior method to perform EEG-based predictions, to the benefit of decision-making researchers and marketing practitioners alike.