BACKGROUND: Atraumatic lower limb amputation is a life-changing event for approximately 185,000 persons in the United States each year. A unilateral amputation is associated with rapid changes to the musculoskeletal system including leg and back muscle atrophy, strength loss, gait asymmetries, differential mechanical joint loading and leg length discrepancies. Even with high-quality medical care and prostheses, amputees still develop secondary musculoskeletal conditions such as chronic low back pain (LBP). Resistance training interventions that focus on core stabilization, lumbar strength and dynamic stability during loading have strong potential to reduce LBP and address amputation-related changes to the musculoskeletal system. Home-based resistance exercise programs may be attractive to patients to minimize travel and financial burdens. METHODS/DESIGN: This study will be a single-assessor-blinded, pre-post-test randomised controlled trial involving 40 men and women aged 18-60 years with traumatic, unilateral transtibial amputation. Participants will be randomised to a home-based, resistance exercise group (HBRX) or a wait-list control group (CON). The HBRX will consist of 12 weeks of elastic resistance band and bodyweight training to improve core and lumbopelvic strength. Participants will be monitored via Skype or Facetime on a weekly basis. The primary outcome will be pain severity (11-point Numerical Pain Rating Scale; NRS DISCUSSION: The study findings will determine whether a HBRX program can decrease pain severity and positively impact several physiological and mechanical factors that contribute to back pain in unilateral transtibial amputees with chronic LBP. We will determine the relative contribution of the exercise-induced changes in these factors on pain responsiveness in this population. TRIAL REGISTRATION: ClinicalTrials.gov, ID: NCT03300375 . Registered on 2 October 2017.