Deep learning methods, and in particular Convolutional Neural Networks (CNNs), have shown breakthrough performance in a wide variety of classification applications, including electroencephalogram-based Brain Computer Interfaces (BCIs). Despite the advances in the field, BCIs are still far from the subject-independent decoding of brain activities, primarily due to substantial inter-subject variability. In this study, we examine the potential application of an ensemble CNN classifier to integrate the capabilities of CNN architectures and ensemble learning for decoding EEG signals collected in motor imagery experiments. The results prove the superiority of the proposed ensemble CNN in comparison with the average base CNN classifiers, with an improvement up to 9% in classification accuracy depending on the test subject. The results also show improvement with respect to the performance of a number of state-of-the-art methods that have been previously used for subject-independent classification in the same datasets used here (i.e., BCI Competition IV 2A and 2B datasets).