Objective The aim of this study was to ascertain the existence of contralateral painful muscle areas mirroring phantom pain and to evaluate the short-term effects of anaesthetics versus saline, injected contralaterally to control phantom and phantom limb pain. Design This was a double-blinded cross-over study. Participants This study included eight lower-limb amputees with phantom limb pain in the past 6 months. Interventions Either 1 ml of 0.25% bupivacaine or 0.9% saline was injected alternately in each point with a 28-G needle, with 72 h between injections. The main outcomes measured were phantom sensation modification and the intensity of phantom limb pain (visual analogue scale) before and after injections. Results Painful muscle areas in the healthy limb do not mirror the topographical distribution of phantom limb pain. At 60 min after the injection, a statistically significantly greater relief of phantom limb pain was observed after using a local anaesthetic compared with that when using saline injection (P = 0.003). Bupivacaine consistently reduced/abolished the phantom sensation in six out of eight patients. These effects on phantom sensation were not observed after saline injections. Conclusion Contralateral injections of 1 ml of 0.25% bupivacaine in the myofascial hyperalgesic areas attenuated phantom limb pain and affected phantom limb sensation. Our study gives a basis of a new method of management of that kind of severe pain to improve the method of rehabilitation of amputee. However, further longitudinal studies with larger number of patients are needed to confirm our study.