Recent developments in the Internet of Things (IoT) and various communication technologies have reshaped numerous application areas. Nowadays, IoT is assimilated into various medical devices and equipment, leading to the progression of the Internet of Medical Things (IoMT). Therefore, various IoMT-based healthcare applications are deployed and used in the day-to-day scenario. Traditionally, machine learning (ML) models use centralized data compilation and learning that is impractical in pragmatic healthcare frameworks due to rising privacy and data security issues. Federated Learning (FL) has been observed as a developing distributed collective paradigm, the most appropriate for modern healthcare framework, that manages various stakeholders (e.g., patients, hospitals, laboratories, etc.) to carry out training of the models without the actual exchange of sensitive medical data. Consequently, in this work, the authors present an exhaustive survey on the security of FL-based IoMT applications in smart healthcare frameworks. First, the authors introduced IoMT devices, their types, applications, datasets, and the IoMT security framework in detail. Subsequently, the concept of FL, its application domains, and various tools used to develop FL applications are discussed. The significant contribution of FL in deploying secure IoMT systems is presented by focusing on FL-based IoMT applications, patents, real-world FL-based healthcare projects, and datasets. A comparison of FL-based security techniques with other schemes in the smart healthcare ecosystem is also presented. Finally, the authors discussed the challenges faced and potential future research recommendations to deploy secure FL-based IoMT applications in smart healthcare frameworks. © 2023 The Author(s)