Background: Most incisions following surgery heal by primary intention, with the edges of the wound apposed with sutures or clips. However, some wounds may break open or be left to heal from the bottom up (i.e. healing by secondary intention). Surgical Wounds Healing by Secondary Intention (SWHSI) are often more complex to manage, and require additional treatments during the course of healing. There is significant uncertainty regarding the best treatment for these complex wounds, with limited robust evidence regarding the clinical and cost-effectiveness of different dressings and treatments; one such treatment is Negative Pressure Wound Therapy (NPWT) which is frequently used in the management of SWHSI. Previous randomised controlled trials (RCTs) of NPWT have failed to recruit to time and target, thus we aimed to conduct a pilot RCT to assess the feasibility of conducting a future, full-scale RCT. Methods: This pilot RCT will test the methods and feasibility of recruiting, randomising, and retaining participants into a larger trial of NPWT verses usual care for patients with SWHSI. Participants will be randomised to receive either NPWT or usual care (no NPWT) and will be followed up for 3 months. Discussion: This study will provide a full assessment of methods for, and feasibility of, recruiting, randomising, and retaining patients with SWHSI in a trial of NPWT versus usual care. On the basis of this pilot trial, a full trial may be proposed in the future which will provide additional, robust evidence on the clinical and cost-effectiveness of NPWT in the management of SWHSI. Trial registration: Clinical Trial Registry: ISRCTN12761776, registered on 10 December 2015 - retrospective registration.