Sweetener type can influence sensory properties and consumer’s acceptance and preference for low-calorie products. An ideal sweetener does not exist, and each sweetener must be used in situations to which it is best suited. Aspartame and sucralose can be good substitutes for sucrose in passion fruit juice. Despite the interest in artificial sweeteners, little is known about how artificial sweeteners are processed in the human brain. Here, we applied the convolutional neural network (CNN) to evaluate brain signals of 11 healthy subjects when they tasted passion fruit juice equivalently sweetened with sucrose (9.4 g/100 g), sucralose (0.01593 g/100 g), or aspartame (0.05477 g/100 g). Electroencephalograms were recorded for two sites in the gustatory cortex (i.e., C3 and C4). Data with artifacts were disregarded, and the artifact-free data were used to feed a Deep Neural Network with tree branches that applied a Convolutions and pooling for different feature filtering and selection. The CNN received raw signal as input for multiclass classification and with supervised training was able to extract underling features and patterns from the signal with better performance than handcrafted filters like FFT. Our results indicated that CNN is an useful tool for electroencephalography (EEG) analyses and classification of perceptually similar tastes.