This modified Reactive Delphi project utilized five rounds of questionnaires to elicit opinion on what would constitute an evidence-based protocol for pilonidal sinus wounds healing by secondary intent, including infected wounds. Participants were health-care professionals including surgeons, nurses and Enterostomal therapy nurses experienced in the care these wounds. Item generation involved an extensive review of the literature to identify key aspects of evidence-based wound care essential to wound healing in general, infected wounds and pilonidal wounds healing by secondary intent, and drawing on clinical experience. The participants responded via an electronic website, using a four-point Likert rating scale and a ranking system. Comments were invited. Feedback to the participants at the end of each round was provided, that included comments, content validity index (CVI), and additional information that provided rationale and references, or minor revision if requested. New items were generated in rounds 3, 4 and 5 in response to participant’s comments. Consensus was confirmed for the items that met the inclusion criteria by further analysis for Confidence Intervals and Kappa Inter-rater Agreement. The resultant protocol contains fifty-nine assessment indicators and interventions, including rationale and an algorithm for decision-making. Topics included treat the cause (surgery/debridement), prevent recurrence, local wound care (cleansing methods, positioning, moist interactive dressings, bacterial balance/ control of chronic inflammation, topical negative pressure therapy for specific criteria), and patient-centred concerns (physical activity, measures to improve hygiene, nutritional interventions and pain management). There is opportunity for further research pertaining to pilonidal sinus wound care to increase the levels of evidence in each area beyond that of expert opinion, and finally to pilot the protocol and determine the outcomes.