Objective To evaluate the effectiveness and advantages of the wide local excision for Paget’s disease involing the penis and scrotum by comparing with the radical excision. Methods A retrospective analysis was made on the clinical data of 41 patients with Paget’s disease involving penis and scrotum who met the inclusion criteria between November 2010 and August 2015. Among them, 14 patients received wide local excision (group A), and 27 patients received radical excision (group B). No significant difference was found in age, course of disease, and lesion site between two groups (P>0.05). The recurrence rate, operative time, times of intraoperative frozen section pathology, hospitalization time, grade of wound healing, appearance and functions satisfaction were recorded and compared between two groups. Results The operative time and hospitalization time in group A were significantly shorter than those in group B (P<0.05); the times of intraoperative frozen section pathology in group A were significantly less than that in group B (P<0.05). All patients were followed up 13 to 67 months (mean, 35.5 months) in group A and 11 to 70 months (mean, 38.8 months) in group B. Grades A, B, and C wound healing was obtained in 11 cases, 2 cases, and 1 case of group A and in 12 cases, 7 cases, and 8 cases of group B respectively, showing significant difference between two groups (Z=–2.102, P=0.036). The 5-year recurrence rate was 28.6% (4/14) in group A and 22.2% (6/27) in group B, showing no significant difference (χ2=0.202, P=0.654). The score of satisfaction in appearance and functions in group A was significantly higher than that in group B (t=–2.810, P=0.008). Conclusion Paget’s disease involving penis and scrotum has a slow disease progression and good prognosis. Wide local excision can relieve symptoms effectively and obviously decrease perioperative risk in elderly patients, with no significant increase of the recurrence rate.