The Health Department released information about the death Tuesday. The first death was in the central part of the state in January.
Cities and details were not disclosed.
Mississippi started reporting statistics about pediatric influenza deaths during the 2007-08 flu season. Since then, 16 people younger than 18 have died of the flu, including the two this year.
The state does not track the number of flu deaths for adults.
Dr. Paul Byers, the state epidemiologist, says the typical peak flu season in the state has passed, but the illness can occur at any time of the year.
Byers says vaccination is the best way to prevent infection.