OBJECTIVE To analyse the clinicopathological characteristics of penoscrotal extramammary Paget’s disease (EMPD) and to discuss the outcomes after frozen section‐guided wide local excision. PATIENTS AND METHODS From 1990 to 2005, at our institution, 38 patients with penoscrotal EMPD received wide local excision with intraoperative frozen‐section analysis. Their medical records were reviewed for patient demographics, lesion characteristics, surgical margin status, and clinical outcome. RESULTS No patients had EMPD secondary to a non‐cutaneous malignancy; 23 patients had intraepithelial EMPD, 12 had invasive EMPD and three had EMPD with underlying adnexal adenocarcinoma. The median (range) largest diameter of the lesion was 6 (1–20) cm. Of 38 patients, 12 (32%) had positive frozen‐section results and had extended surgical excision until a negative margin was obtained. Additional margin examination of the gross specimen and final examination of the frozen sections showed that five patients had false‐negative results. There was a microscopic positive margin in 15 of 38 (40%) patients when a conventional 2 cm clinical tumour‐free border was maintained. Skin erythematous patches were significantly correlated with the spread of disease (P = 0.03). After a median (range) follow‐up of 33.5 (3–140) months, six of 38 (16%) patients had recurrent disease, of whom only two had recurrent skin lesions, while four had systemic progression. CONCLUSION Frozen section‐guided wide local excision gave an acceptable recurrence rate in the treatment of penoscrotal EMPD. Primary EMPD with dermal invasion should be actively monitored for possible aggressive behaviour.