Electroencephalogram Neurofeedback therapy (EEG-NFT) has several potential beneficial effects in terms of improving cognition and electrophysiological regulation among patients with brain injury. However, in vivo structural and functional changes remain less explored. The aim of the present study is to explore EEG-NFT induced in vivo changes in traumatic brain injury (TBI) patients. Two patients with mean age of 15 years with moderate head injury who had more than seven post concussion symptoms and poor cognitive performances (<5 percentile) were subjected to 20 sessions of EEG-NFT. The neuropsychological test scores, post concussion symptoms and MRI scan of the brain were recorded pre-post to EEG-NFT. During EEG-NFT the cognitive scores and concussion symptoms improved significantly (p < 0.05). The EEG-NFT has shown significant increase in cortical grey matter (GM) volumes (p < 0.0001) and fractional anisotropy (FA) of cortical white matter (WM) tracts (p < 0.0001, voxel max 60 and above). There was a significant decrease in global, local efficiency, cost and clustering coefficient of functional connectivity (Wilcoxon Sign Rank Test p < 0.05). Interestingly there was a significant increase in thalamo-cortical connection (increase FA value) after EEG-NFT. The EEG-NFT therapy has shown significant changes in structural and functional connectivity among young moderately injured TBI patients.