Malocclusions are a type of cranio-maxillofacial growth and developmental deformity that occur with high incidence in children. Therefore, a simple and rapid diagnosis of malocclusions would be of great benefit to our future generation. However, the application of deep learning algorithms to the automatic detection of malocclusions in children has not been reported. Therefore, the aim of this study was to develop a deep learning-based method for automatic classification of the sagittal skeletal pattern in children and to validate its performance. This would be the first step in establishing a decision support system for early orthodontic treatment. In this study, four different state-of-the-art (SOTA) models were trained and compared by using 1613 lateral cephalograms, and the best performance model, Densenet-121, was selected was further subsequent validation. Lateral cephalograms and profile photographs were used as the input for the Densenet-121 model, respectively. The models were optimized using transfer learning and data augmentation techniques, and label distribution learning was introduced during model training to address the inevitable label ambiguity between adjacent classes. Five-fold cross-validation was conducted for a comprehensive evaluation of our method. The sensitivity, specificity, and accuracy of the CNN model based on lateral cephalometric radiographs were 83.99, 92.44, and 90.33%, respectively. The accuracy of the model with profile photographs was 83.39%. The accuracy of both CNN models was improved to 91.28 and 83.98%, respectively, while the overfitting decreased after addition of label distribution learning. Previous studies have been based on adult lateral cephalograms. Therefore, our study is novel in using deep learning network architecture with lateral cephalograms and profile photographs obtained from children in order to obtain a high-precision automatic classification of the sagittal skeletal pattern in children.