COVID-19 infection was reported in December 2019 at Wuhan, China. This virus critically affects several countries such as the USA, Brazil, India and Italy. Numerous research units are working at their higher level of effort to develop novel methods to prevent and control this pandemic scenario. The main objective of this paper is to propose a medical decision support system using the implementation of a convolutional neural network (CNN). This CNN has been developed using EfficientNet architecture. To the best of the authors’ knowledge, there is no similar study that proposes an automated method for COVID-19 diagnosis using EfficientNet. Therefore, the main contribution is to present the results of a CNN developed using EfficientNet and 10-fold stratified cross-validation. This paper presents two main experiments. First, the binary classification results using images from COVID-19 patients and normal patients are shown. Second, the multi-class results using images from COVID-19, pneumonia and normal patients are discussed. The results show average accuracy values for binary and multi-class of 99.62% and 96.70%, respectively. On the one hand, the proposed CNN model using EfficientNet presents an average recall value of 99.63% and 96.69% concerning binary and multi-class, respectively. On the other hand, 99.64% is the average precision value reported by binary classification, and 97.54% is presented in multi-class. Finally, the average F1-score for multi-class is 97.11%, and 99.62% is presented for binary classification. In conclusion, the proposed architecture can provide an automated medical diagnostics system to support healthcare specialists for enhanced decision making during this pandemic scenario.