Sorrell Leczkowski, from Adel, Leeds, died after the concert on Monday night and her mother and grandmother are reported to have been left seriously injured.
Elaine Silson, the head of Allerton High School, confirmed the teenager's death in a letter to parents.
Ms Silson said: "I am deeply saddened to have to share with you the news, which has just been confirmed, that one of our Year 9 students, Sorrell Leczkowski, has died as a result of the tragic events at Manchester Arena on Monday night.
"Sorrell was a delightful member of the school community. She enjoyed her studies, had a lovely group of friends and was a real asset to Allerton High School.
"Our whole school community is extremely shocked and saddened by this and our thoughts are with Sorrell's family and friends at this very difficult time."
The headteacher said: "Understandably, our staff and students are very upset and we are receiving support from Leeds City Council, West Yorkshire Police and other external agencies.
"Where appropriate students have been able to speak with experienced staff in a supportive environment. This support will be ongoing."
Ms Silson also included advice to parents in her letter on how to support their children through the tragedy.
Friends of the family have set up an online appeal to help Sorrell's mother, Samantha.
The organiser said: "We are raising funds for Samantha who lost her 14 year old daughter in the atrocities in Manchester last night.
"Samantha is in hospital and we don't want her to worry about getting back to work any time soon.
"RIP Sorrel xxxx."
The appeal was set up to raise Â£1,000 but it soon topped Â£7,000, with more than 380 people donating by Wednesday evening.
To donate to the appeal, go to https://www.justgiving.com/crowdfunding/sarah-smith-123
Reporting from Press Association