Classifying electroencephalography (EEG) signals is an important step for proceeding EEG-based brain computer interfaces (BCI). Currently, kernel based methods such as the support vector machine (SVM) are considered the state-of-the-art methods for this problem. In this paper, we apply Gaussian process (GP) classification to binary discrimination of motor imagery EEG data. Compared with the SVM, GP based methods naturally provide probability outputs for identifying a trusted prediction which can be used for post-processing in a BCI. Experimental results show that the classification methods based on a GP perform similarly to kernel logistic regression and probabilistic SVM in terms of predictive likelihood, but outperform SVM and K-nearest neighbor (KNN) in terms of 0–1 loss class prediction error.