The 11-year-old died in Sunshine Coast University Hospital after catching influenza B last week.
Her death comes after a student on New South Wales' Central Coast died on Tuesday after contracting the influenza virus, just days after health officials urged the community to get vaccinated.
The latest death comes amid a surge in influenza B cases and a high rate of unvaccinated patients as school resumes, Queensland Chief Health Officer John Gerrard said.
He said the state had experienced an influenza A wave leading into winter, but influenza B had taken over as the dominant strain in July.
"There have been three times more hospital admissions for influenza B than influenza A in children aged less than five years," Dr Gerrard said in a statement.
A Sunshine Coast Health spokesperson said in a statement that clinicians were providing support to relatives of the 11-year-old girl.
"We would like to extend our sincere sympathies to the family during this extremely difficult time. This experience is heartbreaking for everyone involved," the spokesperson said.
NSW Chief Health Officer Kerry Chant last week warned circulation of influenza B was rising and young people were at heightened risk from the strain.
