Paediatric endocrinology & diabetes is a sub-specialty which deals with diagnosis, treatment and long-term follow-up of children with endocrine disorders and diabetes. It is a well-reco​gnized sub-specialty in the world and is now also gaining recognition in Pakistan.

The clinical services of paediatric endocrinology & diabetes in this hospital were established in 2009. Over the years it has become a very busy service catering to both inpatients and outpatients. It was initiated in 2018 at Aga Khan University as institutional fellowship. After CPSP approval of this specialty for second fellowship AKU is an accredited site for training.​