This is a report of an innovative influenza immunisation program in three tertiary paediatric hospitals in NSW. A targeted once-off program of influenza immunisation funded by NSW Health was offered during 2010 at the Children’s Hospital at Westmead, Sydney Children’s Hospital and the John Hunter Children’s Hospital. Authorised immunisers offered influenza immunisation to paediatric patients, outpatients and relatives of children with chronic illnesses. Influenza immunisation was administered to 3458 people, 1251 (36%) of whom were children with chronic conditions. In 2009 before the program, 420 influenza vaccines were prescribed for children in two of these hospitals. This number increased to 949 in 2010, the year of the program. Dedicated vaccination clinics at tertiary paediatric hospitals provide additional opportunities to ensure that children at high risk of severe influenza disease and its complications are vaccinated. The information obtained from the hospital vaccination program contributed to the national investigation of febrile convulsions following influenza vaccines in children in 2010.