Epilepsy is a predominant paroxysmal neurological disturbance that is usually recognized as the incidence of impulsive seizures rarely seen in medicine. Automatic detection of epileptic seizures from electroencephalogram (EEG) signals is viewed as an effective diagnosis of patients on the Internet of Medical Things (IoMT). To design a robust detection service in an IoMT environment, the EEG signals of different patients are collected from geographically distributed patients to a centralized server. However, this makes the patient’s privacy prone to exposure and adds to the energy and communication costs. Also, the central server can be subject to malevolent attacks, resulting in non-efficient solutions. In this regard, for the first time, this paper presents a privacy-preserving federated learning framework for epileptic seizure detection (called Fed-ESD) from EEG signals in the fog-computing-based IoMT. A lightweight and efficient spatiotemporal transformer network is introduced to collaboratively learn spatial and temporal representations from the local data of each participant. The proposed Fed-ESD employs geographically situated fog nodes as local aggregators to enable sharing of location-based EEG signals for comparable IoMT applications. Moreover, a greedy method is introduced for deciding on the ideal fog node to be the coordinator node responsible for global aggregation during the training, thereby decreasing the reliance on the central server in the IoMT. Experimental evaluations demonstrate the efficiency of the proposed Fed-ESD in terms of detection performance, resource-efficiency, stability, and scalability for deployment in the IoMT.