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Background: Lipedema is an adipose tissue disorder in women, with an abnormal fat deposition in lower limbs and occasionally upper limbs. The condition is characterized by pain, bruising, heaviness, and mobility impairment. Objectives: This study aims to evaluate the effects of a modified Complete Decongestive Therapy protocol using the Godoy Method in the postoperative period following lipedema surgery. Methods: In total, 293 participants who underwent liposuction for lipedema were studied. The postoperative physiotherapy protocol included Godoy cervical stimuli, Manual Lymphatic Drainage based on Godoy maneuvers, mechanical lymphatic drainage with RAGodoy®, compression with bandages, skin care, and therapeutic education. Results: This study found that the number of physiotherapy sessions significantly reduced pain (p = 0.000) and other complications (p = 0.007) and increased mobility (p = 0.003). The number of physiotherapy sessions showed significant differences in pain intensity at 90 days posttreatment (p = 0.000). In total, 47.24% of the participants became functionally independent on the third day of the physiotherapy intervention (p = 0.003). A total of 40.96% of the participants developed some complications, although a relationship between inadequate compression and the occurrence of complications was also found in 36.52% of patients. Conclusions: The success of surgical treatment for lipedema not only depends on the surgery itself but also on the proper management of the patient in the perioperative period to minimize complications and prevent recurrence. The Complete Decongestive Therapy protocol modified with the Godoy Method showed effects on pain reduction, mobility increase, edema reabsorption, and prevention of complications, consequently enhancing functionality and quality of life for patients undergoing lipedema surgery.