A 71-year-old woman underwent gastrostomy due to malnutrition resulting from impaired esophageal peristalsis due to scleroderma. However, the gastrostomy tube was removed due to worsening of difficult-to-treat dermatitis around the gastrostomy. An intractable gastrocutaneous fistula with persistent gastric juice leakage and peri-gastrostomy dermatitis was treated with fistulotomy and local negative pressure closure therapy under local anesthesia. Spontaneous closure of an intractable fistula after gastrostomy removal can be difficult due to underlying malnutrition and exposure to leaking gastric juice, among other factors. The present case suggests that fistulectomy followed by local negative pressure closure therapy for an intractable fistula after gastrostomy removal can enable oral intake in the early postoperative period and also facilitate wound management.