3-MCC deficiency is among the most common inborn errors of metabolism identified on expanded newborn screening (1:36,000 births). However, evidence-based guidelines for diagnosis and management of this disorder are lacking. Using the traditional Delphi method, a panel of 15 experts in inborn errors of metabolism was convened to develop consensus-based clinical practice guidelines for the diagnosis and management of 3-MCC screen-positive infants and their mothers. The Oxford Centre for Evidence-based Medicine system was used to grade the literature review and create recommendations graded from A (evidence level of randomized clinical trials) to D (expert opinion). Panelists reviewed the initial evaluation of the screen-positive infant-mother dyad, diagnostic guidelines, and management of diagnosed patients. Grade D consensus recommendations were made in each of these three areas. The panel did not reach consensus on all issues. This consensus protocol is intended to assist clinicians in the diagnosis and management of screen-positive newborns for 3-MCC deficiency and to encourage the development of evidence-based guidelines.