Phantom limb pain (PLP) is a challenging condition affecting a significant proportion of amputees. In this article, we describe the case of a 54-year-old Paralympic athlete with phantom limb syndrome following right leg amputation and widespread sports-related enthesitic pain who underwent a whole-body cryostimulation (WBC) cycle, an emerging treatment known for its rapid pain-relieving and anti-inflammatory effects. Assessments were conducted before and after a 10-session WBC cycle, including pain and quality of life assessment and use of medications. A substantial reduction in enthesitic pain, PLP intensity, paresthesia, and tingling related to atmospheric events and improved function and quality of life were reported after the WBC cycle and lasted for two weeks. One month after WBC, the enthesitic pain following sports activity and PLP gradually returned, but with lesser intensity. Similarly, the stump’s sensitivity to atmospheric changes returned, but with lower frequency. Pain at night remained lower than before WBC, with significantly improved quality of sleep. This case study suggests that WBC could be a valuable adjuvant treatment for alleviating PLP. Controlled studies are warranted to validate the findings of this case report and elucidate the mechanisms underlying the positive effects of WBC in this condition.