According to a spokesperson from Alief Independent school district in Houston, the student, Ebony Banks, died on Saturday night.
The teenager's classmates started an online campaign before Ebony's death, to give her a chance to meet her favorite singer.
On Wednesday, the student received a video call from the Grammy winner.
Ebony also received a diploma from her school during a graduation ceremony in the hospital last week.
On Sunday, students gathered at a candlelight vigil to remember Ebony, whose nickname was Ebob.
Videos posted on social media sites show students raising candles to Beyonce's 'Halo.'
Last week, Ebony's friends used the hashtag #EbobMeetsBeyonce in the hopes of attracting Beyonce's attention.
A few days after the hashtag, the singer, who is married to entrepreneur rapper JayZ, surprised Ebony with a video call.
A recording of the conversation between Beyonce and Ebony appeared on the singer's fan pages.
Ebony was seen lying in a hospital bed saying "I love you Beyonce," to which the superstar replies, "I love you."
In a tweet, the school thanked everyone who helped in making Ebony's last wish come true.
Meanwhile, Hollywood gossip sites have claimed that Beyonce is staying away from the public eyes because she is embarrassed about her 'enormous' figure.
"She is just not happy about how much weight she's gained and does not want anyone to see her like this" a source close to the singer is quoted as saying.