Light curve analysis usually involves extracting manually designed features associated with physical parameters and visual inspection. The large amount of data collected nowadays in astronomy by different surveys represents a major challenge of characterizing these signals. Therefore, finding good informative representation for them is a key non-trivial task. Some studies have tried unsupervised machine learning approaches to generate this representation without much effectiveness. In this article, we show that variational auto-encoders can learn these representations by taking the difference between successive timestamps as an additional input. We present two versions of such auto-encoders: Variational Recurrent Auto-Encoder plus time (VRAEt) and re-Scaling Variational Recurrent Auto Encoder plus time (S-VRAEt). The objective is to achieve the most likely low-dimensional representation of the time series that matched latent variables and, in order to reconstruct it, should compactly contain the pattern information. In addition, the S-VRAEt embeds the re-scaling preprocessing of the time series into the model in order to use the Flux standard deviation in the learning of the light curves structure. To assess our approach, we used the largest transit light curve dataset obtained during the 4 years of the Kepler mission and compared to similar techniques in signal processing and light curves. The results show that the proposed methods obtain improvements in terms of the quality of the deep representation of phase-folded transit light curves with respect to their deterministic counterparts. Specifically, they present a good balance between the reconstruction task and the smoothness of the curve, validated with the root mean squared error, mean absolute error, and auto-correlation metrics. Furthermore, there was a good disentanglement in the representation, as validated by the Pearson correlation and mutual information metrics. Finally, a useful representation to distinguish categories was validated with the F1 score in the task of classifying exoplanets. Moreover, the S-VRAEt model increases all the advantages of VRAEt, achieving a classification performance quite close to its maximum model capacity and generating light curves that are visually comparable to a Mandel–Agol fit. Thus, the proposed methods present a new way of analyzing and characterizing light curves.