Background: This study aimed to use a superthin, free superficial circumflex iliac artery perforator (SCIP) flap in functional surgery for treating subungual melanoma and to evaluate its outcomes. Methods: Forty-one patients with primary subungual melanoma of less than or equal to 2-mm thickness who were treated with functional surgery were prospectively enrolled. After oncologic resection, a thin SCIP flap was harvested along the trans-superficial fat layer and transferred to the defect with further thinning by primary defatting. Complications and oncologic outcomes were investigated. Postoperative functional status was assessed, using the Quick Disabilities of the Arm, Shoulder and Hand questionnaire for finger cases and the Foot Function Index for toe cases, and was compared with that of patients treated with amputation. Results: The SCIP flap was inset with a final thickness ranging from 1.5 to 4 mm after defatting. Total flap failure occurred in one patient. Complete wound healing was achieved within 3 weeks postoperatively in most cases (90.2 percent). The majority of patients achieved satisfactory contour without needing secondary debulking. Two recurrences developed during a mean follow-up period of 31 months: one local recurrence and one in-transit recurrence. The 3-year disease-free survival was 97.1 percent. Mean scores for the Quick Disabilities of the Arm, Shoulder and Hand questionnaire and the Foot Function Index following functional surgery were significantly lower than those following amputation. Conclusion: The superthin SCIP flap might serve as a valuable reconstruction option, providing aesthetically thin coverage and reliable outcomes, in functional surgery for treating early-stage subungual melanoma.