This study aimed to develop deep learning models that automatically detect impacted mesiodens on periapical radiographs of primary and mixed dentition using the YOLOv3, RetinaNet, and EfficientDet-D3 algorithms and to compare their performance. Periapical radiographs of 600 pediatric patients (age range, 3–13 years) with mesiodens were used as a training and validation dataset. Deep learning models based on the YOLOv3, RetinaNet, and EfficientDet-D3 algorithms for detecting mesiodens were developed, and each model was trained 300 times using training (540 images) and validation datasets (60 images). The performance of each model was evaluated based on accuracy, sensitivity, and specificity using 120 test images (60 periapical radiographs with mesiodens and 60 periapical radiographs without mesiodens). The accuracy of the YOLOv3, RetinaNet, and EfficientDet-D3 models was 97.5%, 98.3%, and 99.2%, respectively. The sensitivity was 100% for both the YOLOv3 and RetinaNet models and 98.3% for the EfficientDet-D3 model. The specificity was 100%, 96.7%, and 95.0% for the EfficientDet-D3, RetinaNet, and YOLOv3 models, respectively. The proposed models using three deep learning algorithms to detect mesiodens on periapical radiographs showed good performance. The EfficientDet-D3 model showed the highest accuracy for detecting mesiodens on periapical radiographs.