Deep Learning offers flexible powerful tools that have advanced our understanding of the neural coding of neurosensory systems. In this work, a 3D Convolutional Neural Network (3D CNN) is used to mimic the behavior of a population of mice retinal ganglion cells in response to different light patterns. For this purpose, we projected homogeneous RGB flashes and checkerboards stimuli with variable luminances and wavelength spectrum to mimic a more naturalistic stimuli environment onto the mouse retina. We also used white moving bars in order to localize the spatial position of the recorded cells. Then recorded spikes were smoothed with a Gaussian kernel and used as the output target when training a 3D CNN in a supervised way. To find a suitable model, two hyperparameter search stages were performed. In the first stage, a trial and error process allowed us to obtain a system that is able to fit the neurons firing rates. In the second stage, a systematic procedure was used to compare several gradient-based optimizers, loss functions and the model’s convolutional layers number. We found that a three layered 3D CNN was able to predict the ganglion cells firing rates with high correlations and low prediction error, as measured with Mean Squared Error and Dynamic Time Warping in test sets. These models were either competitive or outperformed other models used already in neuroscience, as Feed Forward Neural Networks and Linear-Nonlinear models. This methodology allowed us to capture the temporal dynamic response patterns in a robust way, even for neurons with high trial-to-trial variable spontaneous firing rates, when providing the peristimulus time histogram as an output to our model.