Due to the rapid growth of the information industry, various Internet of Things (IoT) devices have been widely used in our daily lives. Since the demand for low-cost and high-performance hardware devices has increased, malicious third-party vendors may insert malicious circuits into the products to degrade their performance or to leak secret information stored at the devices. The malicious circuit surreptitiously inserted into the hardware products is known as a ‘hardware Trojan.’ How to detect hardware Trojans becomes a significant concern in recent hardware production. In this paper, we propose a hardware Trojan detection method that employs two-stage neural networks and effectively utilizes the Trojan probability of neighbor nets. At the first stage, the 11 Trojan features are extracted from the nets in a given netlist, and then we estimate the Trojan probability that shows the probability of the Trojan nets. At the second stage, we learn the Trojan probability of the neighbor nets for each net in the netlist and classify the nets into a set of normal nets and Trojan ones. The experimental results demonstrate that the average true positive rate becomes 83.6%, and the average true negative rate becomes 96.5%, which is sufficiently high compared to the existing methods.