We present PGTNet, an approach that transforms event logs into graph datasets and leverages graph-oriented data for training Process Graph Transformer Networks to predict the remaining time of business process instances. PGTNet consistently outperforms state-of-the-art deep learning approaches across a diverse range of 20 publicly available real-world event logs. Notably, our approach is most promising for highly complex processes, where existing deep learning approaches encounter difficulties stemming from their limited ability to learn control-flow relationships among process activities and capture long-range dependencies. PGTNet addresses these challenges, while also being able to consider multiple process perspectives during the learning process.