Phantom limb pain (PLP) as neuropathic pain affects the life of amputees. It is believed an efficient PLP treatment should consider the underlying neurological mechanisms. Hereby, we investigated brain activity in PLP and its relationships to the psychological and cognitive dimensions of chronic pain. We investigate differences in resting brain activities between amputees with and without pain. We hypothesize significant differences in the motor cortex and parietal cortex activity that are related to pain perception. Also, we hypothesize two groups have significant differences in cognitive and psychological components. Behavioral assessment (psychological status, life satisfaction, and pain level) and EEG signals of 19 amputees (12 without pain and 7 with pain) were recorded. Data were statistically compared between the two groups. Also, the association between behavioral and neurophysiological data was computed. The results showed a significant decrease in the pain group for the beta and gamma waves, as well as, for the theta and delta waves in the posterior temporal on both sides, during the eye-open condition. The eyes-closed condition showed that the delta waves were decreased on the right side of the cortex. Also, data showed a significant difference in the correlation of pain features with brain waves between the two groups. Significant differences were mostly observed in regions related to pain perception rather than the motor cortex. This can be due to the learned strategies to deal with pain and the degree of pain. Results showed maladaptive cognitive processes had a relationship with brain wave activities. According to the result of brain wave activities, it seems that cognitive factors have a role in the experience of PLP rather than neuroplasticity through amputation. Differences found in the parietal and temporal regions of phantom limb pain's (PLP's) suggests cognition's role in the persistence of PLP.Decreased delta power at the posterior temporal cortex in PLP's could be the focus of treatments.Increased activity of the parietal cortex could be helpful in the treatment of PLP's. PLP is an annoying neurologic pain. A wide range of treatments have focused on this type of pain but couldn't be effective. Recently, researchers suggest BCI-based treatments for better treatment. For this type of treatment, we should know the neurological aspect of PLP. In most studies to investigate or treatment of neurological aspects of PLP, researchers induced pain experimentally or studied acute phantom limb pain. We believed for a better understanding of PLP, should investigate it in a natural and stabilized position. Therefore we studied brain activities in amputees with and without PLP in a resting state to find out differences. Trends in this field express the alpha band differences in the motor cortex. On the contrary, our results showed the most significant difference in high-frequency bandpasses such as beta and gamma. Also, in our study, it seems the parietal and temporal cortex that are related to pain perception is the more relevant to PLP. This study showed a psycho-cognitive aspect of pain such as pain exaggeration has a relation with PLP's brain wave activities. So, we can suggest rather than neuroplasticity through amputation, cognitive factors have a role in the experience of PLP.