As connections from the brain to an external device, Brain-Computer Interface (BCI) systems are a crucial aspect of assisted communication and control. When equipped with well-designed feature extraction and classification approaches, information can be accurately acquired from the brain using such systems. The Hierarchical Extreme Learning Machine (HELM) has been developed as an effective and accurate classification approach due to its deep structure and extreme learning mechanism. A classification system for motor imagery EEG signals is proposed based on the HELM combined with a kernel, herein called the Kernel Hierarchical Extreme Learning Machine (KHELM). Principle Component Analysis (PCA) is used to reduce the dimensionality of the data, and Linear Discriminant Analysis (LDA) is introduced to push the features away from different classes. To demonstrate the performance, the proposed system is applied to the BCI competition 2003 Dataset Ia, and the results are compared with those from state-of-the-art methods; we find that the accuracy is up to 94.54%.