This paper presents a reputation-based threat mitigation framework that defends potential security threats in electroencephalogram (EEG) signal classification during model aggregation of Federated Learning. While EEG signal analysis has attracted attention because of the emergence of brain-computer interface (BCI) technology, it is difficult to create efficient learning models for EEG analysis because of the distributed nature of EEG data and related privacy and security concerns. To address these challenges, the proposed defending framework leverages the Federated Learning paradigm to preserve privacy by collaborative model training with localized data from dispersed sources and introduces a reputation-based mechanism to mitigate the influence of data poisoning attacks and identify compromised participants. To assess the efficiency of the proposed reputation-based federated learning defense framework, data poisoning attacks based on the risk level of training data derived by Explainable Artificial Intelligence (XAI) techniques are conducted on both publicly available EEG signal datasets and the self-established EEG signal dataset. Experimental results on the poisoned datasets show that the proposed defense methodology performs well in EEG signal classification while reducing the risks associated with security threats.