Purpose: Cone beam computed tomography (CBCT) is widely used to evaluate the temporomandibular joint (TMJ). For the three-dimensional (3D) assessment of the TMJ, segmentation of the mandibular condyle and articular fossa is essential. This study aimed to perform deep learning-based 3D segmentation of the mandibular condyle on CBCT images and evaluate the performance of the segmentation. Methods: CBCT scan data from 99 patients (mean age: 53.3±19.2 years) diagnosed with TMJ disorders were analyzed. From the CBCT images, sagittal, coronal, and axial planes showing the mandibular condyle were selected and combined to form two-dimensional (2D) images. The U-Net deep learning model was used to exclusively segment the mandibular condyle area from the 2D images. From these results, 3D images of the mandibular condyle were reconstructed. Accuracy, precision, recall, and the Dice coefficient were calculated to appraise segmentation performance in each plane. Results: The average Dice coefficient was 0.92 for the coronal and axial planes and 0.82 for the sagittal plane. The CBCT image-based segmentation performance of the mandibular condyle in the coronal and axial planes exceeded that in the sagittal plane. The sharpness and uniformity of the 2D images affected segmentation performance,...