Stroke is a world-leading disease for causing disability. Brain-computer interaction (BCI) training has been proved to be a promising method in facilitating motor recovery. However, due to differences in each patient's neural-clinical profile, the potential of recovery for different patients can vary significantly by conducting BCI training, which remains a major problem in clinical rehabilitation practice. To address this issue, the objective of this study is to prognosticate the outcome of BCI training using motor state electroencephalographic (EEG) collected during the first session of BCI tasks, with the aim of prescribing BCI training accordingly. A Convolution Neural Network (CNN) based prognosis model was developed to predict the outcome of 11 stroke patients' recovery following a 2-week rehabilitation training with BCI. In our study, functional connectivity and power spectrum have been evaluated and applied as the inputs of CNN to regress patients' recovery rate. A saliency map was used to identify the correlation between EEG channels with the recovery outcome. The performance of our model was assessed using the leave-one-out cross-validation. Overall, the proposed model predicted patients' recovery with R 2 0.98 and MSE 0.89. According to the saliency map, the highest functional connectivity occurred in Fp2/Fpz-AF8, Fp2/F4/F8-P3, P1/PO7-PO5 and AF3-AF4. Our results demonstrated that deep learning method has the potential to predict the recovery rate of BCI training, which contributes to guiding individualized prescription in the early stage of clinical rehabilitation.