Dhaka Shishu Hospital comprises three major divisions e.g. Paediatric Medicine, Paediatric Surgey, Anaesthesia and the Diagnostic Division. Paediatric Medicine consists of Cardiology, Nephrology, Neurology, Child Development & Child Pschycology, Neonatology, Gastroenterology, Hepatology and Nutrition, Haematology-oncology & Thalassemia, Respiratory Medicine, Endocrinology & Metabolic Disorder, Infectious Diseases and Community Paediatrics, General Paediatrics. Paediatric Surgery includes Neonatal Surgery, Urology, Burn & Reconstuctive Surgery, Paediatric Orthopaedics, Traumatology, Surgical Oncology, Laparoscopy and ENT Surgery. Diagnostic division includes Microbiology, Clinical Pathology, Biochemistry, Radiology & Imaging.

The intensive Care Unit (ICU) for children, the first of its kind in Bangladesh was established in this hospital in 1992. It has Day Care Centre, Observation & Referral Unit & a well equipped Physiotherpy Department.

The OPD and the Emergency handle a 900-1000 of paediatric patients daily. The OPD includes Medicine,  Surgery, ENT, Skin, Dentistry, EPI, CDC, Breast feeding counseling and various follow up clinics. Follow up clinics include Cardiology, Nephrology, Child Development Centre, Neonatology, Growth and Nutrition, TB and Endocrinology. The hospital has two special centres such as Thalassaemia Centre and CDC where patients are receiving specialized treatment. Five beds have been reserved in the Infectious Disease and Community Paediatrics Unit for emergency outbreak e.g. Diarrhoea, Dengue Fever and Swine Flu.