(1) Background: The COVID-19 pandemic has generated 771 million confirmed cases. Of these patients, 60% have developed persistent symptoms including pain. This pain is a complex symptom that needs comprehensive therapeutic strategies to address it holistically. The main objective of this study will be to evaluate the early impact of the Pain Informed Movement (PIM) program in patients with post-COVID-19 conditions experiencing new-onset persistent pain. (2) Methods: A randomized, single-blind clinical trial will be performed. Patients will be randomly assigned (1:1) to the experimental or control group. The experimental group will undergo a PIM program consisting of low-intensity functional exercises, pain neuroscience education, and relaxation techniques. The control group will receive no intervention. (3) Results: The results will be published as a peer-reviewed article. (4) Conclusions: This study will provide a basis for future research to support the implementation of comprehensive therapeutic approaches in the care of patients with post-COVID-19 persistent pain.