Phantom limb pain (PLP) may be relieved using a visual representation of an intact limb. However, patients with distorted (telescoped) phantoms seem unable to associate with visualizations of intact limbs. A virtual arm visualization was matched to the individual's phantom perception and controlled in an augmented reality (AR) intervention. Seven PLP participants with telescoped phantoms performed eight supervised home-based AR-training sessions (45 min each) within two weeks. The virtual arm was superimposed in AR onto their residual limb and controlled using electromyography from the residual limb. AR-training sessions included three AR-tasks aimed at reengaging the neural circuits related to the lost limb. Agency (Rubber hand illusion questionnaire) and telescoping (proprioceptive drift and felt telescoping) were monitored after individual training sessions. fMRI during lip pursing was assessed before and after intervention. Pain rating index scores were reduced by 52% (mean change= -1.884, p= 0.032, d = 1.135). Numerical rating scale scores of PLP severity (0-6), in patients benefitting from the intervention, were reduced by 41% (mean change = 0.93 p = 0.022, d = 1.334). The lip pursing task illustrated decreased cortical activity in the primary somatosensory cortex, which correlated to the reduced NRS scores of PLP severity. Perspective: Two weeks of novel AR interventions in patients with telescoped phantoms demonstrated reduced PLP and reversal of cortical reorganization. This research highlights the potential of individualized AR interventions for PLP and indicate the importance of agency in this type of treatments.