Primary care physicians, particularly pediatricians, are expected to promote physical activity and prescribe exercise to patients. Unfortunately, many health care professionals do not have adequate skills or experience in this area, making exercise intervention logistically and psychologically challenging. Exercise-deficit disorder (EDD), which is a new term to the literature, is defined as reduced levels of moderate-to-vigorous physical activity, inconsistent with public health recommendations. Physicians are in a unique position to identify children who are deficient in exercise and initiate prevention strategies. To aid physicians in the diagnosis and treatment of children with EDD, we propose integrating exercise assessment into primary care practice, and, when appropriate, referral to a pediatric exercise specialist. This approach should ensure adequate development of muscle strength and motor skills that are required for successful physical activity participation. The timely identification of children with EDD is essential in preventing resistance to intervention. Connecting pediatric health care professionals with pediatric exercise specialists, culminating in an established professional collaborative system, is critical for promoting healthy behaviors throughout childhood and adolescence.