Phantom limb pain is attributed to abnormal sensorimotor cortical representations. Various feedback treatments have been applied to induce the reorganization of the sensorimotor cortical representations to reduce pain. We developed a training protocol using a brain-computer interface (BCI) to induce plastic changes in the sensorimotor cortical representation of phantom hand movements and demonstrated that BCI training effectively reduces phantom limb pain. By comparing the induced cortical representation and pain, the mechanisms worsening the pain have been attributed to the residual phantom hand representation. Based on our data obtained using neurofeedback training without explicit phantom hand movements and hand-like visual feedback, we suggest a direct relationship between cortical representation and pain. In this review, we summarize the results of our BCI training protocol and discuss the relationship between cortical representation and phantom limb pain. We propose a treatment for phantom limb pain based on real-time neuroimaging to induce appropriate cortical reorganization by monitoring cortical activities.