The presence of point defects such as vacancies plays an important role in material design. Here, we demonstrate that a graph neural network (GNN) model trained only on perfect materials can also be used to predict vacancy formation energies (E vac ) of defect structures without the need for additional training data. Such GNN-based predictions are considerably faster than density functional theory (DFT) calculations with reasonable accuracy and show the potential that GNNs are able to capture a functional form for energy predictions. To test this strategy, we developed a DFT dataset of 508 E vac consisting of 3D elemental solids, alloys, oxides, nitrides, and 2D monolayer materials. We analyzed and discussed the applicability of such direct and fast predictions. We applied the model to predict 192494 E vac for 55723 materials in the JARVIS-DFT database.Defects play an important role in our pursuit to engineer performance of a material. Vacancies are a type of defects which are ubiquitous and their presence can significantly alter 1