Background Pilonidal sinus is a common health problem. The current study aimed to compare the impact of autologous platelet-rich plasma (PRP) with that of minimally invasive techniques in terms of pain reduction, return to daily activities, quality of life, and duration of wound healing after open excision and secondary closure. Methods Patients who were over 18 years old and had chronic PS disease between March 2018 and January 2019 were enrolled and randomly divided into three groups. Open surgery and moist dressings were applied to patients in group A. Open surgery followed by PRP application was performed on patients in group B. Group C underwent curettage of the sinus cavity followed by application of PRP. In this prospective randomized controlled study, patients completed questionnaires (including the Nottingham Health Profile (NHP), Short Form-36 (SF-36) and clinical information) before and after surgery. Demographics, preoperative characteristics, healing parameters, and quality-of-life scores were evaluated and calculated before and after surgery. Results and conclusion The cavity volume and wound-healing time were compared among the groups on postoperative days 0, 2, 3, 4, and 21. Each patient was followed up throughout the process of wound healing, and follow-up was continued afterward to monitor the patients for recurrence. Due to the nature of the treatment that group C received, this group achieved shorter healing times and smaller cavity volume than the other groups. In contrast, the recovery time per unit of cavity volume was significantly faster in group B than in the other groups. Overall postoperative pain scores were significantly lower for both PRP groups (open surgery, group B; minimally invasive surgery, group C) than for group A (p < 0.001) and showed different time courses among the groups. In the treatment of PS disease, PRP application improves postoperative recovery in that it speeds patients' return to daily activities, reduces their pain scores and increases their quality of life. Trial registration The current study is registered on the public website ClinicalTrials.gov (ClinicalTrials.gov identifier number: NCT04697082; date: 05/01/2021).