The Internet of Things (IoT) has tremendous success in health care, smart city, industrial production and so on. Protected agriculture is one of the fields which has broad application prospects of IoT. Protected agriculture is a mode of highly efficient development of modern agriculture that uses artificial techniques to change climatic factors such as temperature, to create environmental conditions suitable for the growth of animals and plants. This review aims to gain insight into the state-of-the-art of IoT applications in protected agriculture and to identify the system structure and key technologies. Therefore, we completed a systematic literature review of IoT research and deployments in protected agriculture over the past 10 years and evaluated the contributions made by different academicians and organizations. Selected references were clustered into three application domains corresponding to plant management, animal farming and food/agricultural product supply traceability. Furthermore, we discussed the challenges along with future research prospects, to help new researchers of this domain understand the current research progress of IoT in protected agriculture and to propose more novel and innovative ideas in the future.