The diagnosis and treatment of epilepsy is a significant direction for both machine learning and brain science. This paper newly proposes a fast enhanced exemplar-based clustering (FEEC) method for incomplete EEG signal. The algorithm first compresses the potential exemplar list and reduces the pairwise similarity matrix. By processing the most complete data in the first stage, FEEC then extends the few incomplete data into the exemplar list. A new compressed similarity matrix will be constructed and the scale of this matrix is greatly reduced. Finally, FEEC optimizes the new target function by the enhanced α-expansion move method. On the other hand, due to the pairwise relationship, FEEC also improves the generalization of this algorithm. In contrast to other exemplar-based models, the performance of the proposed clustering algorithm is comprehensively verified by the experiments on two datasets.