This paper presents a novel automatic facial expressions recognition system (AFERS) using the deep network framework. The proposed AFERS consists of four steps: 1) geometric features extraction; 2) regional local binary pattern (LBP) features extraction; 3) fusion of both the features using autoencoders; and 4) classification using Kohonen self-organizing map (SOM)-based classifier. This paper makes three distinct contributions. The proposed deep network consisting of autoencoders and the SOM-based classifier is computationally more efficient and performance wise more accurate. The fusion of geometric features with LBP features using autoencoders provides better representation of facial expression. The SOM-based classifier proposed in this paper has been improved by making use of a soft-threshold logic and a better learning algorithm. The performance of the proposed approach is validated on two widely used databases (DBs): 1) MMI and 2) extended Cohn-Kanade (CK+). An average recognition accuracy of 97.55% in MMI DB and 98.95% in CK+ DB are obtained using the proposed algorithm. The recognition results obtained from fused features are found to be distinctly superior to both recognition using individual features as well as recognition with a direct concatenation of the individual feature vectors. Simulation results validate that the proposed AFERS is more efficient as compared to the existing approaches.