Considerable progress has been made in saving the lives of children younger than 5 years. Nevertheless, these advances have failed to help all children thrive, particularly children with disabilities. We describe the increasing prevalence of disability among children and adolescents. We evaluate the current situation regarding children with disabilities and rehabilitation in the context of health systems, particularly those in low- and middle-income countries. Within the newborn health agenda, congenital anomalies often require early intervention and rehabilitation. We provide Argentina as an example of a country where rehabilitation for congenital anomalies is integrated into the health system. We argue that congenital anomalies that require rehabilitation have the potential to strengthen rehabilitation systems and policies by: strengthening coordination between primary care and rehabilitation; identifying and understanding pathways that allow families to engage with services; providing human resources for rehabilitation; and building systems and resources that support assistive technology and rehabilitation. We propose ways for countries to prioritize and integrate early identification, referral and care for children with congenital anomalies to strengthen health systems for all. We identify opportunities to expand policy and planning and to design service delivery and workforce strategies through World Health Organization guidelines and frameworks for rehabilitation. We argue that the global health community must act to ensure that rehabilitation services to support functioning from birth are well established, accepted and integrated within health systems, and that disability is prioritized within child health. These steps would strengthen health systems, ensure functioning from birth and make rehabilitation accessible to all.