GNE myopathy is a rare disease, and there are no case reports of treatment for GNE myopathy with comorbid head and neck cancer. In the case presented here, we performed reconstruction using a free flap for patient with tongue cancer and comorbid GNE myopathy. Preservation of normal trunk and upper limb function via flap transplantation from a paralytic lower limb is a reasonable proposition. Several cases of harvesting flaps from polio infection-related paralytic limbs have been reported, and we observed similar findings to those reports in our case. With careful attention to the fibrosis of the connective tissue, harvesting flaps from paralytic limbs is a viable option and can be used safely.