Background: Access to essential medicines in pediatric endocrinology and diabetes is limited in resource-limited countries. The World Health Organization (WHO) maintains two non-binding lists of essential medicines (EMLs) which are often used as a template for developing national EMLs. Methods: We compared a previously published master list of medicines for pediatric endocrinology and diabetes with the WHO EMLs and national EMLs for countries within the WHO African region. To better understand actual access to medicines by patients, we focused on diabetes and surveyed pediatric endocrinologists from 5 countries and assessed availability and true cost for insulin and glucagon. Results: Most medicines that are essential in pediatric endocrinology and diabetes were included in the national EMLs. However, essential medicines, such as fludrocortisone, were present in less than 30% of the national EMLs despite being recommended by the WHO. Pediatric endocrinologists from the 5 focus countries reported significant variation in terms of availability and public access to insulin, as well as differences between urban and rural areas. Except for Botswana, glucagon was rarely available. There was no significant relationship between Gross National Income and the number of medicines included in the national EMLs. Conclusions: Governments in resource-limited countries could take further steps to improve EMLs and access to medicines such as improved collaboration between health authorities, the pharmaceutical industry, patient groups, health professionals, and capacity-building programs such as Paediatric Endocrinology Training Centres for Africa.