The participation of third-party entities in the globalized semiconductor supply chain introduces potential security vulnerabilities, such as intellectual property piracy and hardware Trojan (HT) insertion. Graph neural networks (GNNs) have been employed to address various hardware security threats, owing to their superior performance on graph-structured data, such as circuits. However, GNNs are also susceptible to attacks. This work examines the use of GNNs for detecting hardware threats like HTs and their vulnerability to attacks. We present BadGNN, a backdoor attack on GNNs that can hide HTs and evade detection with a 100% success rate through minor circuit perturbations. Our findings highlight the need for further investigation into the security and robustness of GNNs before they can be safely used in security-critical applications.