The confirmed outbreak at Les Quennevais School comes just a week after a girl at Beaulieu School was struck down by the virus. Tests on a pupil at La Moye School who fell ill last week returned negative.
The Health Department said that Les Quennevais School would remain open, and parents and children in the same class as the pupils had been informed of the outbreak.
Staff from the school and Public Health Department visited the secondary school yesterday and were due to attend again today to offer advice to the children.
All pupils who have been in close contact with the two pupils will also be offered the anti-viral drug Tamiflu.
A flu helpline, which offers general information about the disease, is available on 445566 from Monday to Friday between 8.30 am and 5.30 pm.