In this paper, we propose a lightweight physical layer aided authentication and key agreement (PL-AKA) protocol in the internet of things (IoT). Conventional evolved packet system AKA (EPS-AKA) used in long-term evolution (LTE) systems may suffer from congestions in core networks by the large signaling overhead as the number of IoT devices increases. Thus, in order to alleviate the overhead, we consider a cross-layer authentication by integrating physical layer approaches to cryptography-based schemes. To demonstrate the feasibility of the PL-AKA, universal software radio peripheral (USRP) based tests are conducted as well as numerical simulations. The proposed scheme shows a significant reduction in signaling overhead compared to the conventional EPS-AKA in both simulation and experiment. Therefore, the proposed lightweight PL-AKA has the potential for practical and efficient implementation of large-scale IoT networks.