Disclosed herein are an apparatus and method for authenticating an IoT device. The method, performed by the IoT device authentication apparatus, includes transmitting, by the IoT device authentication apparatus, a random number to the IoT device and encrypting, by the IoT device authentication apparatus, the random number using a previously registered first white-box cryptography value through a white-box cryptography method; generating, by the IoT device, a first device response value from a previously registered first device challenge value using a Physical Unclonable Function (PUF) and encrypting, by the IoT device, the random number, received from the IoT device authentication apparatus, using the first device response value; and performing, by the IoT device authentication apparatus, authentication of the IoT device by checking whether the random number encrypted using the white-box cryptography method matches the random number encrypted using the PUF, which is received from the IoT device.