Early detection and classification of pulmonary nodules using computer-aided diagnosis (CAD) systems is useful in reducing mortality rates of lung cancer. In this paper, we propose a new deep learning method to improve classification accuracy of pulmonary nodules in computed tomography (CT) scans. Our method uses a novel 15-layer 2D deep convolutional neural network architecture for automatic feature extraction and classification of pulmonary candidates as nodule or nonnodule. Focal loss function is then applied to the training process to boost classification accuracy of the model. We evaluated our method on the LIDC/IDRI dataset extracted by the LUNA16 challenge. The experiments showed that our deep learning method with focal loss is a high-quality classifier with an accuracy of 97.2%, sensitivity of 96.0%, and specificity of 97.3%.