Three-dimensional facial stereophotogrammetry provides a detailed representation of craniofacial soft tissue without the use of ionizing radiation. While manual annotation of landmarks serves as the current gold standard for cephalometric analysis, it is a time-consuming process and is prone to human error. The aim in this study was to develop and evaluate an automated cephalometric annotation method using a deep learning-based approach. Ten landmarks were manually annotated on 2897 3D facial photographs. The automated landmarking workflow involved two successive DiffusionNet models. The dataset was randomly divided into a training and test dataset. The precision of the workflow was evaluated by calculating the Euclidean distances between the automated and manual landmarks and compared to the intra-observer and inter-observer variability of manual annotation and a semi-automated landmarking method. The workflow was successful in 98.6% of all test cases. The deep learning-based landmarking method achieved precise and consistent landmark annotation. The mean precision of 1.69 ± 1.15 mm was comparable to the inter-observer variability (1.31 ± 0.91 mm) of manual annotation. Automated landmark annotation on 3D photographs was achieved with the DiffusionNet-based approach. The proposed method allows quantitative analysis of large datasets and may be used in diagnosis, follow-up, and virtual surgical planning.