The analysis of non-stationary signals commonly includes the signal segmentation process, dividing such signals into smaller time series, which are considered stationary and thus easier to process. Most commonly, the methods for signal segmentation utilize complex filtering, transformation and feature extraction techniques together with various kinds of classifiers, which especially in the field of biomedical signals, do not perform very well and are generally prone to poor performance when dealing with signals obtained in highly variable environments. In order to address these problems, we designed a new method for the segmentation of heart sound signals using deep convolutional neural networks, which works in a straightforward automatic manner and does not require any complex pre-processing. The proposed method was tested on a set of heartbeat sound clips, collected by non-experts with mobile devices in highly variable environments with excessive background noise. The obtained results show that the proposed method outperforms other methods, which are taking advantage of using domain knowledge for the analysis of the signals. Based on the encouraging experimental results, we believe that the proposed method can be considered as a solid basis for the further development of the automatic segmentation of highly variable signals using deep neural networks.