The number of devices connected to the Internet is increasing as the Internet of Things (IoT) technologies are evolving. The increasing number of the Internet connected IoT devices result in highly increasing amount of exposing data, thereby increasing privacy invasion and threat of survival as well. Therefore, security in the IoT service must be provided. Recently, there have been several hacking attacks mainly targeting small devices that do not change an initially configured default password. To respond to these security threats, devices must be securely configured. However, most of the small devices that are deployed for IoT service have restricted user interface (UI). Moreover, general users have difficulties in performing initial configuration safely because of their lack of security knowledge. Also, in order to provide secure IoT services, a new IoT device and an authentication server which register the device are to be mutually authenticated each other. In this paper, we propose a method to perform mutual authentication between the new device and the authentication server by using NFC as an additional communication channel and to securely configure the registration and initialization key of the IoT device.