Despite favourable outcomes in recurrence after off-midline closure techniques in pilonidal surgery, between 18% and 40% of patients suffer from prolonged postoperative wound healing. The aim of this work was to investigate if closed-incision negative-pressure wound therapy (NPWT) promotes wound healing after Bascom's cleft lift (BCL) surgery for complicated pilonidal sinus disease compared with conventional drainage and dressing. Patients were randomized to either NPWT for 4-7 days or loop-vessel drain for 24 h and a dry dressing postoperatively. Healing was evaluated by a wound care nurse blinded for randomization at 2 and 12 weeks postoperatively (primary endpoint). Healing was defined as one or no closing defects of ≤5 mm and with no undermining. Although we had wanted to recruit 200 patients, the study was terminated at 118 patients (NPWT group, n = 60; control group, n = 58) after interim analysis. Patients were comparable by age, sex, body mass index, previous smoking status and indication for BCL surgery. At 2 weeks 12% of patients were healed in both the NPWT and control groups [risk difference = 0.00(95% CI -0.12 to 0.11), p = 1.00]. After 12 weeks, 68% of patients were healed in the NPWT group and 72% in the control group [risk difference = -0.03 (95% CI 0.19 to 0.13), p = 0.82]. There was no significant difference in pain experienced postsurgery. In a symptom-based questionnaire, the control group reported self-esteem to be less affected (p = 0.015). Closed-incision negative-pressure wound therapy did not significantly improve healing after BCL surgery for complicated pilonidal sinus disease.