Last year, the flu vaccine was recommended for those six months to 5 years old.
The Health Department said it is taking the lead from the federal Centers for Disease Control and Prevention in making the recommendation.
The CDC changed the recommendation after finding that children often spread influenza to others.
Influenza is a highly contagious respiratory illness. People 65 and older and infants and children are at highest risk of complications.
The Health Department says that in 2006, more than 4,000 children up to age 10 were hospitalized due to influenza and pneumonia; 10 children under 14 died.