Background Phantom limb pain (PLP) is a chronic condition that can greatly diminish quality of life. Purposeful control over the phantom limb activates of the affected neural circuitry and leads to dissolution of the pathological relationship linking sensorimotor and pain processing (which gives rise to PLP). An international, double-blind, randomized controlled clinical trial (RCT) on the use of phantom motor execution (PME) as a treatment for PLP is currently undertaken, where PME is compared to active placebo. Methods and design Sixty-seven subjects suffering from PLP in upper or lower limbs are randomly assigned in 2:1 ratio to PME or phantom motor imagery (PMI) interventions respectively. Subjects allocated to either treatment receive 15 interventions and are exposed to the same VR-AR environments using the same device. The only difference between interventions is whether phantom movements are performed (PME) or just imagined (PMI). Results The primary outcome of the study is to examine whether 15 sessions of PME can induce a greater PLP relief, compared to PMI. The secondary objectives are to examine whether 15 sessions of PME provide a greater improvement on different aspects related to PLP compared to PMI, such as pain duration, pain intensity as measured by other metrics and the patient’s own impression about the effect of treatment. Long-term retention of treatment benefits will be assessed as change in all the variables (both primary and secondary) between baseline and follow-up timepoints (at one-, three- and six-months post treatment). Conclusion This manuscript serves as the formal statistical analysis plan (version 1.0) for the international, double-blind, randomized controlled clinical trial on the use of phantom motor execution as a treatment for phantom limb pain. The statistical analysis plan was completed on 3 August 2021. Trial registration number NCT03112928. SAP version Version: 1.0 Date: 2021/08/03 Protocol Version This document has been written based on information contained in the study protocol published in [1], in July 2018. SAP Revisions Not applicable