The disclosed systems and methods provide for a mirror box therapy system as a therapeutic tool for treating patients having one healthy and one unhealthy limb. This can include stroke patients or those whom otherwise have full or partial paralysis. Also suitable patients include amputees with phantom limb pain or those with intact legs whom have unilateral chronic lower extremity pain. The system is designed to be used with patients in the short sit position or long sit position and can be alternated between each position including switching between left side and right side limb treatment. The methods of treatment with the disclosed system are designed to provide for positive visual feedback and induce brain plasticity with the improvement of neural connections leading to pain and/or motor rehabilitation of the impaired limb.