Background The recurrence rate of extramammary Paget disease after surgical resection is high due to the lesions' poorly delineated and unclear margins. Aims To evaluate the impact of non-invasive tumour margin detection via photodynamic diagnosis plus reflectance confocal microscopy on the surgical outcomes of patients with extramammary Paget disease. Methods Thirty-six patients with histopathologically confirmed primary extramammary Paget disease between January 2017 and June 2018 were included in this study. The skin lesion margins were preoperatively observed using the naked eye, photodynamic diagnosis, and reflectance confocal microscopy. An incision was made 0.5-2 cm from the outermost non-invasive detection marker line. The incision depth was more significant than the follicle level or the deepest level affected by the tumour in the biopsy specimens. After the skin lesions were removed, a pathological examination of the specimens was conducted to ensure clear margins to prevent tumour recurrence and metastases. Results A total of 166 good-quality tissue sections were selected from 36 patients. The tumour surfaces and deep margins were within the scope of resection. Six patients (6/36, 15.4%) experienced local recurrence 2-12 months postoperatively. One patient (1/36, 2.8%) had lymph node metastasis without local recurrence 36 months postoperatively and died 50 months postoperatively (1/36, 2.8%). Limitations This study is limited by the small patient population, especially the number of patients with mucous membrane involvement. Conclusion Using photodynamic diagnosis plus reflectance confocal microscopy to detect the margins of extramammary Paget disease lesions non-invasively reduces the postoperative tumour recurrence rate and is a valuable guide for tumour treatment.